catherine authored on 24/04/2021 22:14:36 | ... | ... |
@@ -40,12 +40,14 @@ for fedup pathway enrichment analysis. Current file formats supported are |
| 40 | 40 |
gmt, txt, and xlsx. |
| 41 | 41 |
} |
| 42 | 42 |
\examples{
|
| 43 |
+# Generate pathway list from GMT annotation file |
|
| 43 | 44 |
pathways <- readPathways( |
| 44 | 45 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 45 | 46 |
package = "fedup" |
| 46 | 47 |
), |
| 47 | 48 |
minGene = 10, maxGene = 500 |
| 48 | 49 |
) |
| 50 |
+# Generate pathway list from XLSX annotation file |
|
| 49 | 51 |
pathways <- readPathways( |
| 50 | 52 |
system.file("extdata", "SAFE_terms.xlsx", package = "fedup"),
|
| 51 | 53 |
header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID" |
Catherine Ross authored on 23/03/2021 23:37:33 | ... | ... |
@@ -2,8 +2,7 @@ |
| 2 | 2 |
% Please edit documentation in R/pathways.R |
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 |
-\title{Returns a list of pathways from various file formats.
|
|
| 6 |
-Currently supports the following file format: gmt, txt, xlsx.} |
|
| 5 |
+\title{Returns a list of pathways from various file formats.}
|
|
| 7 | 6 |
\usage{
|
| 8 | 7 |
readPathways( |
| 9 | 8 |
pathwayFile, |
| ... | ... |
@@ -15,29 +14,30 @@ readPathways( |
| 15 | 14 |
) |
| 16 | 15 |
} |
| 17 | 16 |
\arguments{
|
| 18 |
-\item{pathwayFile}{(char) path to file with pathway annotations.}
|
|
| 17 |
+\item{pathwayFile}{(char) path to file with pathway annotations}
|
|
| 19 | 18 |
|
| 20 | 19 |
\item{header}{(logical) whether \code{pathwayFile} has a header
|
| 21 |
-(default FALSE).} |
|
| 20 |
+(default FALSE)} |
|
| 22 | 21 |
|
| 23 |
-\item{pathCol}{(char or int) column name or number with pathway identifiers.
|
|
| 24 |
-For use with non-GMT input files (eg "Pathway.ID" or 2; default NULL).} |
|
| 22 |
+\item{pathCol}{(char or int) column name or number with pathway identifiers
|
|
| 23 |
+(for use with non-GMT input files (eg "Pathway.ID" or 2; default NULL))} |
|
| 25 | 24 |
|
| 26 |
-\item{geneCol}{(char or int) column name or number with gene identifiers.
|
|
| 27 |
-For use with non-GMT input files (eg "Gene.ID" or 5; default NULL).} |
|
| 25 |
+\item{geneCol}{(char or int) column name or number with gene identifiers
|
|
| 26 |
+(for use with non-GMT input files (eg "Gene.ID" or 5; default NULL))} |
|
| 28 | 27 |
|
| 29 | 28 |
\item{minGene}{(integer) minimum number of genes to be considered
|
| 30 |
-in a pathway (default 1).} |
|
| 29 |
+in a pathway (default 1)} |
|
| 31 | 30 |
|
| 32 | 31 |
\item{maxGene}{(integer) maximum number of genes to be considered
|
| 33 |
-in a pathway (default Inf).} |
|
| 32 |
+in a pathway (default Inf)} |
|
| 34 | 33 |
} |
| 35 | 34 |
\value{
|
| 36 |
-a list of vectors with pathway annotations. |
|
| 35 |
+A list of vectors with pathway annotations. |
|
| 37 | 36 |
} |
| 38 | 37 |
\description{
|
| 39 |
-Returns a list of pathways from various file formats. |
|
| 40 |
-Currently supports the following file format: gmt, txt, xlsx. |
|
| 38 |
+This function supports custom pathway annotations to use |
|
| 39 |
+for fedup pathway enrichment analysis. Current file formats supported are |
|
| 40 |
+gmt, txt, and xlsx. |
|
| 41 | 41 |
} |
| 42 | 42 |
\examples{
|
| 43 | 43 |
pathways <- readPathways( |
Catherine Ross authored on 05/03/2021 23:01:00 | ... | ... |
@@ -6,12 +6,12 @@ |
| 6 | 6 |
Currently supports the following file format: gmt, txt, xlsx.} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 |
- pathwayFile, |
|
| 10 |
- header = FALSE, |
|
| 11 |
- pathCol = NULL, |
|
| 12 |
- geneCol = NULL, |
|
| 13 |
- minGene = 1L, |
|
| 14 |
- maxGene = Inf |
|
| 9 |
+ pathwayFile, |
|
| 10 |
+ header = FALSE, |
|
| 11 |
+ pathCol = NULL, |
|
| 12 |
+ geneCol = NULL, |
|
| 13 |
+ minGene = 1L, |
|
| 14 |
+ maxGene = Inf |
|
| 15 | 15 |
) |
| 16 | 16 |
} |
| 17 | 17 |
\arguments{
|
Catherine Ross authored on 21/02/2021 05:36:05 | ... | ... |
@@ -42,12 +42,12 @@ Currently supports the following file format: gmt, txt, xlsx. |
| 42 | 42 |
\examples{
|
| 43 | 43 |
pathways <- readPathways( |
| 44 | 44 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 45 |
- package = "FEDUP" |
|
| 45 |
+ package = "fedup" |
|
| 46 | 46 |
), |
| 47 | 47 |
minGene = 10, maxGene = 500 |
| 48 | 48 |
) |
| 49 | 49 |
pathways <- readPathways( |
| 50 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 50 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "fedup"),
|
|
| 51 | 51 |
header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID" |
| 52 | 52 |
) |
| 53 | 53 |
} |
Catherine Ross authored on 18/02/2021 20:45:03 | ... | ... |
@@ -8,7 +8,7 @@ Currently supports the following file format: gmt, txt, xlsx.} |
| 8 | 8 |
readPathways( |
| 9 | 9 |
pathwayFile, |
| 10 | 10 |
header = FALSE, |
| 11 |
- pathwayCol = NULL, |
|
| 11 |
+ pathCol = NULL, |
|
| 12 | 12 |
geneCol = NULL, |
| 13 | 13 |
minGene = 1L, |
| 14 | 14 |
maxGene = Inf |
| ... | ... |
@@ -20,11 +20,11 @@ readPathways( |
| 20 | 20 |
\item{header}{(logical) whether \code{pathwayFile} has a header
|
| 21 | 21 |
(default FALSE).} |
| 22 | 22 |
|
| 23 |
-\item{pathwayCol}{(char) column name with pathway identifiers.
|
|
| 24 |
-For use with non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 23 |
+\item{pathCol}{(char or int) column name or number with pathway identifiers.
|
|
| 24 |
+For use with non-GMT input files (eg "Pathway.ID" or 2; default NULL).} |
|
| 25 | 25 |
|
| 26 |
-\item{geneCol}{(char) column name with gene identifiers.
|
|
| 27 |
-For use with non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 26 |
+\item{geneCol}{(char or int) column name or number with gene identifiers.
|
|
| 27 |
+For use with non-GMT input files (eg "Gene.ID" or 5; default NULL).} |
|
| 28 | 28 |
|
| 29 | 29 |
\item{minGene}{(integer) minimum number of genes to be considered
|
| 30 | 30 |
in a pathway (default 1).} |
| ... | ... |
@@ -48,6 +48,6 @@ pathways <- readPathways( |
| 48 | 48 |
) |
| 49 | 49 |
pathways <- readPathways( |
| 50 | 50 |
system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
| 51 |
- header = TRUE, pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID" |
|
| 51 |
+ header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID" |
|
| 52 | 52 |
) |
| 53 | 53 |
} |
Catherine Ross authored on 12/02/2021 21:24:28 | ... | ... |
@@ -42,8 +42,12 @@ Currently supports the following file format: gmt, txt, xlsx. |
| 42 | 42 |
\examples{
|
| 43 | 43 |
pathways <- readPathways( |
| 44 | 44 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 45 |
- package="FEDUP"), minGene=10, maxGene=500) |
|
| 45 |
+ package = "FEDUP" |
|
| 46 |
+ ), |
|
| 47 |
+ minGene = 10, maxGene = 500 |
|
| 48 |
+) |
|
| 46 | 49 |
pathways <- readPathways( |
| 47 |
- system.file("extdata", "SAFE_terms.xlsx", package="FEDUP"),
|
|
| 48 |
- header=TRUE, pathwayCol="Enriched.GO.names", geneCol="Gene.ID") |
|
| 50 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 51 |
+ header = TRUE, pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID" |
|
| 52 |
+) |
|
| 49 | 53 |
} |
Catherine Ross authored on 12/02/2021 06:50:44 | ... | ... |
@@ -3,47 +3,47 @@ |
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 | 5 |
\title{Returns a list of pathways from various file formats.
|
| 6 |
-Currently supports the following file format: GMT, TXT, XLSX.} |
|
| 6 |
+Currently supports the following file format: gmt, txt, xlsx.} |
|
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 |
- pathway_file, |
|
| 9 |
+ pathwayFile, |
|
| 10 | 10 |
header = FALSE, |
| 11 |
- pathway_col = NULL, |
|
| 12 |
- gene_col = NULL, |
|
| 13 |
- MIN_GENE = 1L, |
|
| 14 |
- MAX_GENE = Inf |
|
| 11 |
+ pathwayCol = NULL, |
|
| 12 |
+ geneCol = NULL, |
|
| 13 |
+ minGene = 1L, |
|
| 14 |
+ maxGene = Inf |
|
| 15 | 15 |
) |
| 16 | 16 |
} |
| 17 | 17 |
\arguments{
|
| 18 |
-\item{pathway_file}{(char) path to file with pathway annotations.}
|
|
| 18 |
+\item{pathwayFile}{(char) path to file with pathway annotations.}
|
|
| 19 | 19 |
|
| 20 |
-\item{header}{(logical) whether \code{pathway_file} has a header
|
|
| 20 |
+\item{header}{(logical) whether \code{pathwayFile} has a header
|
|
| 21 | 21 |
(default FALSE).} |
| 22 | 22 |
|
| 23 |
-\item{pathway_col}{(char) column name with pathway identifiers.
|
|
| 23 |
+\item{pathwayCol}{(char) column name with pathway identifiers.
|
|
| 24 | 24 |
For use with non-GMT input files (eg "Pathway.ID"; default NULL).} |
| 25 | 25 |
|
| 26 |
-\item{gene_col}{(char) column name with gene identifiers.
|
|
| 26 |
+\item{geneCol}{(char) column name with gene identifiers.
|
|
| 27 | 27 |
For use with non-GMT input files (eg "Gene.ID"; default NULL).} |
| 28 | 28 |
|
| 29 |
-\item{MIN_GENE}{(integer) minimum number of genes to be considered
|
|
| 30 |
-in a pathway (default = 1).} |
|
| 29 |
+\item{minGene}{(integer) minimum number of genes to be considered
|
|
| 30 |
+in a pathway (default 1).} |
|
| 31 | 31 |
|
| 32 |
-\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
|
| 33 |
-in a pathway (default = Inf).} |
|
| 32 |
+\item{maxGene}{(integer) maximum number of genes to be considered
|
|
| 33 |
+in a pathway (default Inf).} |
|
| 34 | 34 |
} |
| 35 | 35 |
\value{
|
| 36 | 36 |
a list of vectors with pathway annotations. |
| 37 | 37 |
} |
| 38 | 38 |
\description{
|
| 39 | 39 |
Returns a list of pathways from various file formats. |
| 40 |
-Currently supports the following file format: GMT, TXT, XLSX. |
|
| 40 |
+Currently supports the following file format: gmt, txt, xlsx. |
|
| 41 | 41 |
} |
| 42 | 42 |
\examples{
|
| 43 | 43 |
pathways <- readPathways( |
| 44 | 44 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 45 |
- package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 45 |
+ package="FEDUP"), minGene=10, maxGene=500) |
|
| 46 | 46 |
pathways <- readPathways( |
| 47 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 48 |
- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID") |
|
| 47 |
+ system.file("extdata", "SAFE_terms.xlsx", package="FEDUP"),
|
|
| 48 |
+ header=TRUE, pathwayCol="Enriched.GO.names", geneCol="Gene.ID") |
|
| 49 | 49 |
} |
Former-commit-id: 4d51792bca083f02938e7375225eff324d219c86
Catherine Ross authored on 11/02/2021 07:27:35 | ... | ... |
@@ -11,12 +11,7 @@ readPathways( |
| 11 | 11 |
pathway_col = NULL, |
| 12 | 12 |
gene_col = NULL, |
| 13 | 13 |
MIN_GENE = 1L, |
| 14 |
-<<<<<<< HEAD |
|
| 15 | 14 |
MAX_GENE = Inf |
| 16 |
-======= |
|
| 17 |
- MAX_GENE = Inf, |
|
| 18 |
- GO_class = NULL |
|
| 19 |
->>>>>>> 00991f87a2a7f1e9145a31acc65e1f9ed16d9363 |
|
| 20 | 15 |
) |
| 21 | 16 |
} |
| 22 | 17 |
\arguments{
|
| ... | ... |
@@ -36,12 +31,6 @@ in a pathway (default = 1).} |
| 36 | 31 |
|
| 37 | 32 |
\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
| 38 | 33 |
in a pathway (default = Inf).} |
| 39 |
-<<<<<<< HEAD |
|
| 40 |
-======= |
|
| 41 |
- |
|
| 42 |
-\item{GO_class}{(char) if GO terms are present in \code{pathway_file},
|
|
| 43 |
-which class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 44 |
->>>>>>> 00991f87a2a7f1e9145a31acc65e1f9ed16d9363 |
|
| 45 | 34 |
} |
| 46 | 35 |
\value{
|
| 47 | 36 |
a list of vectors with pathway annotations. |
Former-commit-id: 603e9281202cf5a276c7c1a612264fd350efa501
Catherine Ross authored on 11/02/2021 07:21:45 Former-commit-id: 3fc088bec88f63f8dbe1c83f960586edc2cb3d00
Catherine Ross authored on 11/02/2021 07:18:35 | ... | ... |
@@ -11,8 +11,7 @@ readPathways( |
| 11 | 11 |
pathway_col = NULL, |
| 12 | 12 |
gene_col = NULL, |
| 13 | 13 |
MIN_GENE = 1L, |
| 14 |
- MAX_GENE = Inf, |
|
| 15 |
- GO_class = NULL |
|
| 14 |
+ MAX_GENE = Inf |
|
| 16 | 15 |
) |
| 17 | 16 |
} |
| 18 | 17 |
\arguments{
|
| ... | ... |
@@ -32,9 +31,6 @@ in a pathway (default = 1).} |
| 32 | 31 |
|
| 33 | 32 |
\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
| 34 | 33 |
in a pathway (default = Inf).} |
| 35 |
- |
|
| 36 |
-\item{GO_class}{(char) if GO terms are present in \code{pathway_file},
|
|
| 37 |
-which class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 38 | 34 |
} |
| 39 | 35 |
\value{
|
| 40 | 36 |
a list of vectors with pathway annotations. |
Former-commit-id: 04af82691b9ada33877c0ff4d1ee4455e520ee11
Catherine Ross authored on 10/02/2021 07:10:06 | ... | ... |
@@ -7,7 +7,7 @@ Currently supports the following file format: GMT, TXT, XLSX.} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 | 9 |
pathway_file, |
| 10 |
- header = TRUE, |
|
| 10 |
+ header = FALSE, |
|
| 11 | 11 |
pathway_col = NULL, |
| 12 | 12 |
gene_col = NULL, |
| 13 | 13 |
MIN_GENE = 1L, |
| ... | ... |
@@ -18,13 +18,14 @@ readPathways( |
| 18 | 18 |
\arguments{
|
| 19 | 19 |
\item{pathway_file}{(char) path to file with pathway annotations.}
|
| 20 | 20 |
|
| 21 |
-\item{header}{(logical) whether pathway_file has a header (default TRUE).}
|
|
| 21 |
+\item{header}{(logical) whether \code{pathway_file} has a header
|
|
| 22 |
+(default FALSE).} |
|
| 22 | 23 |
|
| 23 | 24 |
\item{pathway_col}{(char) column name with pathway identifiers.
|
| 24 |
-For use with for non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 |
+For use with non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 | 26 |
|
| 26 | 27 |
\item{gene_col}{(char) column name with gene identifiers.
|
| 27 |
-For use with for non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 |
+For use with non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 | 29 |
|
| 29 | 30 |
\item{MIN_GENE}{(integer) minimum number of genes to be considered
|
| 30 | 31 |
in a pathway (default = 1).} |
| ... | ... |
@@ -32,8 +33,8 @@ in a pathway (default = 1).} |
| 32 | 33 |
\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
| 33 | 34 |
in a pathway (default = Inf).} |
| 34 | 35 |
|
| 35 |
-\item{GO_class}{(char) if GO terms are present in `pathway_file`, which
|
|
| 36 |
-class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 36 |
+\item{GO_class}{(char) if GO terms are present in \code{pathway_file},
|
|
| 37 |
+which class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 37 | 38 |
} |
| 38 | 39 |
\value{
|
| 39 | 40 |
a list of vectors with pathway annotations. |
| ... | ... |
@@ -44,10 +45,9 @@ Currently supports the following file format: GMT, TXT, XLSX. |
| 44 | 45 |
} |
| 45 | 46 |
\examples{
|
| 46 | 47 |
pathways <- readPathways( |
| 47 |
- system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 48 |
- package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 48 |
+ system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 49 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 49 | 50 |
pathways <- readPathways( |
| 50 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 51 |
- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
|
| 52 |
- MIN_GENE = 10, MAX_GENE = 500) |
|
| 51 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 52 |
+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID") |
|
| 53 | 53 |
} |
Former-commit-id: 6c9cb5c25c50990937f6f4fad54168326755e9ee
Catherine Ross authored on 10/02/2021 07:10:06 | ... | ... |
@@ -7,7 +7,7 @@ Currently supports the following file format: GMT, TXT, XLSX.} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 | 9 |
pathway_file, |
| 10 |
- header = TRUE, |
|
| 10 |
+ header = FALSE, |
|
| 11 | 11 |
pathway_col = NULL, |
| 12 | 12 |
gene_col = NULL, |
| 13 | 13 |
MIN_GENE = 1L, |
| ... | ... |
@@ -18,13 +18,14 @@ readPathways( |
| 18 | 18 |
\arguments{
|
| 19 | 19 |
\item{pathway_file}{(char) path to file with pathway annotations.}
|
| 20 | 20 |
|
| 21 |
-\item{header}{(logical) whether pathway_file has a header (default TRUE).}
|
|
| 21 |
+\item{header}{(logical) whether \code{pathway_file} has a header
|
|
| 22 |
+(default FALSE).} |
|
| 22 | 23 |
|
| 23 | 24 |
\item{pathway_col}{(char) column name with pathway identifiers.
|
| 24 |
-For use with for non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 |
+For use with non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 | 26 |
|
| 26 | 27 |
\item{gene_col}{(char) column name with gene identifiers.
|
| 27 |
-For use with for non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 |
+For use with non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 | 29 |
|
| 29 | 30 |
\item{MIN_GENE}{(integer) minimum number of genes to be considered
|
| 30 | 31 |
in a pathway (default = 1).} |
| ... | ... |
@@ -32,8 +33,8 @@ in a pathway (default = 1).} |
| 32 | 33 |
\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
| 33 | 34 |
in a pathway (default = Inf).} |
| 34 | 35 |
|
| 35 |
-\item{GO_class}{(char) if GO terms are present in `pathway_file`, which
|
|
| 36 |
-class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 36 |
+\item{GO_class}{(char) if GO terms are present in \code{pathway_file},
|
|
| 37 |
+which class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 37 | 38 |
} |
| 38 | 39 |
\value{
|
| 39 | 40 |
a list of vectors with pathway annotations. |
| ... | ... |
@@ -44,10 +45,9 @@ Currently supports the following file format: GMT, TXT, XLSX. |
| 44 | 45 |
} |
| 45 | 46 |
\examples{
|
| 46 | 47 |
pathways <- readPathways( |
| 47 |
- system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 48 |
- package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 48 |
+ system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 49 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 49 | 50 |
pathways <- readPathways( |
| 50 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 51 |
- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
|
| 52 |
- MIN_GENE = 10, MAX_GENE = 500) |
|
| 51 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 52 |
+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID") |
|
| 53 | 53 |
} |
Former-commit-id: 8963930bbc9b73fe0e3785708d466695c5144f93
Catherine Ross authored on 05/02/2021 23:28:08 | ... | ... |
@@ -2,55 +2,52 @@ |
| 2 | 2 |
% Please edit documentation in R/pathways.R |
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 |
-\title{Returns a list of pathways from a variety of file formats.
|
|
| 6 |
-Currently supports the following file format: GMT, TXT, XLSX} |
|
| 5 |
+\title{Returns a list of pathways from various file formats.
|
|
| 6 |
+Currently supports the following file format: GMT, TXT, XLSX.} |
|
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 | 9 |
pathway_file, |
| 10 | 10 |
header = TRUE, |
| 11 |
- pathway_col, |
|
| 12 |
- gene_col, |
|
| 11 |
+ pathway_col = NULL, |
|
| 12 |
+ gene_col = NULL, |
|
| 13 | 13 |
MIN_GENE = 1L, |
| 14 | 14 |
MAX_GENE = Inf, |
| 15 | 15 |
GO_class = NULL |
| 16 | 16 |
) |
| 17 | 17 |
} |
| 18 | 18 |
\arguments{
|
| 19 |
-\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 19 |
+\item{pathway_file}{(char) path to file with pathway annotations.}
|
|
| 20 | 20 |
|
| 21 |
-\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 21 |
+\item{header}{(logical) whether pathway_file has a header (default TRUE).}
|
|
| 22 | 22 |
|
| 23 |
-\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 24 |
-use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 23 |
+\item{pathway_col}{(char) column name with pathway identifiers.
|
|
| 24 |
+For use with for non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 | 25 |
|
| 26 |
-\item{gene_col}{(char) column name with gene identifiers
|
|
| 27 |
-use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 26 |
+\item{gene_col}{(char) column name with gene identifiers.
|
|
| 27 |
+For use with for non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 | 28 |
|
| 29 |
-\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 30 |
-(default = 1)} |
|
| 29 |
+\item{MIN_GENE}{(integer) minimum number of genes to be considered
|
|
| 30 |
+in a pathway (default = 1).} |
|
| 31 | 31 |
|
| 32 |
-\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 33 |
-(default = Inf)} |
|
| 32 |
+\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
|
| 33 |
+in a pathway (default = Inf).} |
|
| 34 | 34 |
|
| 35 |
-\item{GO_class}{(char) if GO terms are present in 'pathway_file', which
|
|
| 36 |
-class(es) should be subsetted (i.e., BP, MF, CC) |
|
| 37 |
-(default = NULL)} |
|
| 35 |
+\item{GO_class}{(char) if GO terms are present in `pathway_file`, which
|
|
| 36 |
+class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 38 | 37 |
} |
| 39 | 38 |
\value{
|
| 40 |
-a list of vectors with pathway annotations |
|
| 39 |
+a list of vectors with pathway annotations. |
|
| 41 | 40 |
} |
| 42 | 41 |
\description{
|
| 43 |
-Returns a list of pathways from a variety of file formats. |
|
| 44 |
-Currently supports the following file format: GMT, TXT, XLSX |
|
| 42 |
+Returns a list of pathways from various file formats. |
|
| 43 |
+Currently supports the following file format: GMT, TXT, XLSX. |
|
| 45 | 44 |
} |
| 46 | 45 |
\examples{
|
| 47 | 46 |
pathways <- readPathways( |
| 48 | 47 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 49 |
- package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500 |
|
| 50 |
-) |
|
| 48 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 51 | 49 |
pathways <- readPathways( |
| 52 | 50 |
system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
| 53 | 51 |
header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
| 54 |
- MIN_GENE = 10, MAX_GENE = 500 |
|
| 55 |
-) |
|
| 52 |
+ MIN_GENE = 10, MAX_GENE = 500) |
|
| 56 | 53 |
} |
Former-commit-id: 6f876229b0af1113b79d5b357b6378af7c95222f
Catherine Ross authored on 05/02/2021 23:28:08 | ... | ... |
@@ -2,55 +2,52 @@ |
| 2 | 2 |
% Please edit documentation in R/pathways.R |
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 |
-\title{Returns a list of pathways from a variety of file formats.
|
|
| 6 |
-Currently supports the following file format: GMT, TXT, XLSX} |
|
| 5 |
+\title{Returns a list of pathways from various file formats.
|
|
| 6 |
+Currently supports the following file format: GMT, TXT, XLSX.} |
|
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 | 9 |
pathway_file, |
| 10 | 10 |
header = TRUE, |
| 11 |
- pathway_col, |
|
| 12 |
- gene_col, |
|
| 11 |
+ pathway_col = NULL, |
|
| 12 |
+ gene_col = NULL, |
|
| 13 | 13 |
MIN_GENE = 1L, |
| 14 | 14 |
MAX_GENE = Inf, |
| 15 | 15 |
GO_class = NULL |
| 16 | 16 |
) |
| 17 | 17 |
} |
| 18 | 18 |
\arguments{
|
| 19 |
-\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 19 |
+\item{pathway_file}{(char) path to file with pathway annotations.}
|
|
| 20 | 20 |
|
| 21 |
-\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 21 |
+\item{header}{(logical) whether pathway_file has a header (default TRUE).}
|
|
| 22 | 22 |
|
| 23 |
-\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 24 |
-use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 23 |
+\item{pathway_col}{(char) column name with pathway identifiers.
|
|
| 24 |
+For use with for non-GMT input files (eg "Pathway.ID"; default NULL).} |
|
| 25 | 25 |
|
| 26 |
-\item{gene_col}{(char) column name with gene identifiers
|
|
| 27 |
-use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 26 |
+\item{gene_col}{(char) column name with gene identifiers.
|
|
| 27 |
+For use with for non-GMT input files (eg "Gene.ID"; default NULL).} |
|
| 28 | 28 |
|
| 29 |
-\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 30 |
-(default = 1)} |
|
| 29 |
+\item{MIN_GENE}{(integer) minimum number of genes to be considered
|
|
| 30 |
+in a pathway (default = 1).} |
|
| 31 | 31 |
|
| 32 |
-\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 33 |
-(default = Inf)} |
|
| 32 |
+\item{MAX_GENE}{(integer) maximum number of genes to be considered
|
|
| 33 |
+in a pathway (default = Inf).} |
|
| 34 | 34 |
|
| 35 |
-\item{GO_class}{(char) if GO terms are present in 'pathway_file', which
|
|
| 36 |
-class(es) should be subsetted (i.e., BP, MF, CC) |
|
| 37 |
-(default = NULL)} |
|
| 35 |
+\item{GO_class}{(char) if GO terms are present in `pathway_file`, which
|
|
| 36 |
+class(es) should be subsetted (BP, MF and/or CC, default NULL).} |
|
| 38 | 37 |
} |
| 39 | 38 |
\value{
|
| 40 |
-a list of vectors with pathway annotations |
|
| 39 |
+a list of vectors with pathway annotations. |
|
| 41 | 40 |
} |
| 42 | 41 |
\description{
|
| 43 |
-Returns a list of pathways from a variety of file formats. |
|
| 44 |
-Currently supports the following file format: GMT, TXT, XLSX |
|
| 42 |
+Returns a list of pathways from various file formats. |
|
| 43 |
+Currently supports the following file format: GMT, TXT, XLSX. |
|
| 45 | 44 |
} |
| 46 | 45 |
\examples{
|
| 47 | 46 |
pathways <- readPathways( |
| 48 | 47 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 49 |
- package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500 |
|
| 50 |
-) |
|
| 48 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500) |
|
| 51 | 49 |
pathways <- readPathways( |
| 52 | 50 |
system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
| 53 | 51 |
header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
| 54 |
- MIN_GENE = 10, MAX_GENE = 500 |
|
| 55 |
-) |
|
| 52 |
+ MIN_GENE = 10, MAX_GENE = 500) |
|
| 56 | 53 |
} |
Former-commit-id: f10b80ebf948d722a8773104b6d6bc41e7a2644b
Catherine Ross authored on 29/01/2021 23:17:47 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,56 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/pathways.R |
|
| 3 |
+\name{readPathways}
|
|
| 4 |
+\alias{readPathways}
|
|
| 5 |
+\title{Returns a list of pathways from a variety of file formats.
|
|
| 6 |
+Currently supports the following file format: GMT, TXT, XLSX} |
|
| 7 |
+\usage{
|
|
| 8 |
+readPathways( |
|
| 9 |
+ pathway_file, |
|
| 10 |
+ header = TRUE, |
|
| 11 |
+ pathway_col, |
|
| 12 |
+ gene_col, |
|
| 13 |
+ MIN_GENE = 1L, |
|
| 14 |
+ MAX_GENE = Inf, |
|
| 15 |
+ GO_class = NULL |
|
| 16 |
+) |
|
| 17 |
+} |
|
| 18 |
+\arguments{
|
|
| 19 |
+\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 20 |
+ |
|
| 21 |
+\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 22 |
+ |
|
| 23 |
+\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 24 |
+use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 25 |
+ |
|
| 26 |
+\item{gene_col}{(char) column name with gene identifiers
|
|
| 27 |
+use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 28 |
+ |
|
| 29 |
+\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 30 |
+(default = 1)} |
|
| 31 |
+ |
|
| 32 |
+\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 33 |
+(default = Inf)} |
|
| 34 |
+ |
|
| 35 |
+\item{GO_class}{(char) if GO terms are present in 'pathway_file', which
|
|
| 36 |
+class(es) should be subsetted (i.e., BP, MF, CC) |
|
| 37 |
+(default = NULL)} |
|
| 38 |
+} |
|
| 39 |
+\value{
|
|
| 40 |
+a list of vectors with pathway annotations |
|
| 41 |
+} |
|
| 42 |
+\description{
|
|
| 43 |
+Returns a list of pathways from a variety of file formats. |
|
| 44 |
+Currently supports the following file format: GMT, TXT, XLSX |
|
| 45 |
+} |
|
| 46 |
+\examples{
|
|
| 47 |
+pathways <- readPathways( |
|
| 48 |
+ system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 49 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500 |
|
| 50 |
+) |
|
| 51 |
+pathways <- readPathways( |
|
| 52 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 53 |
+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
|
| 54 |
+ MIN_GENE = 10, MAX_GENE = 500 |
|
| 55 |
+) |
|
| 56 |
+} |
Former-commit-id: 0ef905fee4bf648953d9a4f6dcb3a09a07a09abd
Catherine Ross authored on 29/01/2021 23:17:47 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,56 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/pathways.R |
|
| 3 |
+\name{readPathways}
|
|
| 4 |
+\alias{readPathways}
|
|
| 5 |
+\title{Returns a list of pathways from a variety of file formats.
|
|
| 6 |
+Currently supports the following file format: GMT, TXT, XLSX} |
|
| 7 |
+\usage{
|
|
| 8 |
+readPathways( |
|
| 9 |
+ pathway_file, |
|
| 10 |
+ header = TRUE, |
|
| 11 |
+ pathway_col, |
|
| 12 |
+ gene_col, |
|
| 13 |
+ MIN_GENE = 1L, |
|
| 14 |
+ MAX_GENE = Inf, |
|
| 15 |
+ GO_class = NULL |
|
| 16 |
+) |
|
| 17 |
+} |
|
| 18 |
+\arguments{
|
|
| 19 |
+\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 20 |
+ |
|
| 21 |
+\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 22 |
+ |
|
| 23 |
+\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 24 |
+use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 25 |
+ |
|
| 26 |
+\item{gene_col}{(char) column name with gene identifiers
|
|
| 27 |
+use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 28 |
+ |
|
| 29 |
+\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 30 |
+(default = 1)} |
|
| 31 |
+ |
|
| 32 |
+\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 33 |
+(default = Inf)} |
|
| 34 |
+ |
|
| 35 |
+\item{GO_class}{(char) if GO terms are present in 'pathway_file', which
|
|
| 36 |
+class(es) should be subsetted (i.e., BP, MF, CC) |
|
| 37 |
+(default = NULL)} |
|
| 38 |
+} |
|
| 39 |
+\value{
|
|
| 40 |
+a list of vectors with pathway annotations |
|
| 41 |
+} |
|
| 42 |
+\description{
|
|
| 43 |
+Returns a list of pathways from a variety of file formats. |
|
| 44 |
+Currently supports the following file format: GMT, TXT, XLSX |
|
| 45 |
+} |
|
| 46 |
+\examples{
|
|
| 47 |
+pathways <- readPathways( |
|
| 48 |
+ system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
|
| 49 |
+ package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500 |
|
| 50 |
+) |
|
| 51 |
+pathways <- readPathways( |
|
| 52 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 53 |
+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID", |
|
| 54 |
+ MIN_GENE = 10, MAX_GENE = 500 |
|
| 55 |
+) |
|
| 56 |
+} |
Catherine Ross authored on 20/11/2020 21:42:53 | 1 | 1 |
deleted file mode 100644 |
| ... | ... |
@@ -1,49 +0,0 @@ |
| 1 |
-% Generated by roxygen2: do not edit by hand |
|
| 2 |
-% Please edit documentation in R/pathways.R |
|
| 3 |
-\name{readPathways}
|
|
| 4 |
-\alias{readPathways}
|
|
| 5 |
-\title{Returns a list of pathways from a file.
|
|
| 6 |
-Currently supports the following file format: GMT, TXT, XLSX} |
|
| 7 |
-\usage{
|
|
| 8 |
-readPathways( |
|
| 9 |
- pathway_file, |
|
| 10 |
- header = TRUE, |
|
| 11 |
- pathway_col, |
|
| 12 |
- gene_col, |
|
| 13 |
- MIN_GENE = 10L, |
|
| 14 |
- MAX_GENE = 500L |
|
| 15 |
-) |
|
| 16 |
-} |
|
| 17 |
-\arguments{
|
|
| 18 |
-\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 19 |
- |
|
| 20 |
-\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 21 |
- |
|
| 22 |
-\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 23 |
-use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 24 |
- |
|
| 25 |
-\item{gene_col}{(char) column name with gene identifiers, one gene per row
|
|
| 26 |
-use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 27 |
- |
|
| 28 |
-\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 29 |
-(default = 10)} |
|
| 30 |
- |
|
| 31 |
-\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 32 |
-(default = 500)} |
|
| 33 |
-} |
|
| 34 |
-\value{
|
|
| 35 |
-a list of vectors with pathways |
|
| 36 |
-} |
|
| 37 |
-\description{
|
|
| 38 |
-Returns a list of pathways from a file. |
|
| 39 |
-Currently supports the following file format: GMT, TXT, XLSX |
|
| 40 |
-} |
|
| 41 |
-\examples{
|
|
| 42 |
-pathways <- readPathways( |
|
| 43 |
- system.file("extdata", "YeastDatabase_GO_gmt.gmt", package = "FEDUP")
|
|
| 44 |
-) |
|
| 45 |
-pathways <- readPathways( |
|
| 46 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 47 |
- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "ORF.ID" |
|
| 48 |
-) |
|
| 49 |
-} |
Catherine Ross authored on 20/11/2020 21:42:53 | 1 | 1 |
deleted file mode 100644 |
| ... | ... |
@@ -1,49 +0,0 @@ |
| 1 |
-% Generated by roxygen2: do not edit by hand |
|
| 2 |
-% Please edit documentation in R/pathways.R |
|
| 3 |
-\name{readPathways}
|
|
| 4 |
-\alias{readPathways}
|
|
| 5 |
-\title{Returns a list of pathways from a file.
|
|
| 6 |
-Currently supports the following file format: GMT, TXT, XLSX} |
|
| 7 |
-\usage{
|
|
| 8 |
-readPathways( |
|
| 9 |
- pathway_file, |
|
| 10 |
- header = TRUE, |
|
| 11 |
- pathway_col, |
|
| 12 |
- gene_col, |
|
| 13 |
- MIN_GENE = 10L, |
|
| 14 |
- MAX_GENE = 500L |
|
| 15 |
-) |
|
| 16 |
-} |
|
| 17 |
-\arguments{
|
|
| 18 |
-\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 19 |
- |
|
| 20 |
-\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 21 |
- |
|
| 22 |
-\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 23 |
-use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 24 |
- |
|
| 25 |
-\item{gene_col}{(char) column name with gene identifiers, one gene per row
|
|
| 26 |
-use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 27 |
- |
|
| 28 |
-\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 29 |
-(default = 10)} |
|
| 30 |
- |
|
| 31 |
-\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 32 |
-(default = 500)} |
|
| 33 |
-} |
|
| 34 |
-\value{
|
|
| 35 |
-a list of vectors with pathways |
|
| 36 |
-} |
|
| 37 |
-\description{
|
|
| 38 |
-Returns a list of pathways from a file. |
|
| 39 |
-Currently supports the following file format: GMT, TXT, XLSX |
|
| 40 |
-} |
|
| 41 |
-\examples{
|
|
| 42 |
-pathways <- readPathways( |
|
| 43 |
- system.file("extdata", "YeastDatabase_GO_gmt.gmt", package = "FEDUP")
|
|
| 44 |
-) |
|
| 45 |
-pathways <- readPathways( |
|
| 46 |
- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 47 |
- header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "ORF.ID" |
|
| 48 |
-) |
|
| 49 |
-} |
Catherine Ross authored on 03/11/2020 22:52:32 | ... | ... |
@@ -1,8 +1,8 @@ |
| 1 | 1 |
% Generated by roxygen2: do not edit by hand |
| 2 |
-% Please edit documentation in R/readPathways.R |
|
| 2 |
+% Please edit documentation in R/pathways.R |
|
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 |
-\title{Returns a list of pathways from a file
|
|
| 5 |
+\title{Returns a list of pathways from a file.
|
|
| 6 | 6 |
Currently supports the following file format: GMT, TXT, XLSX} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| ... | ... |
@@ -35,7 +35,7 @@ use for non-GMT input (eg "Gene.ID", default = NULL)} |
| 35 | 35 |
a list of vectors with pathways |
| 36 | 36 |
} |
| 37 | 37 |
\description{
|
| 38 |
-Returns a list of pathways from a file |
|
| 38 |
+Returns a list of pathways from a file. |
|
| 39 | 39 |
Currently supports the following file format: GMT, TXT, XLSX |
| 40 | 40 |
} |
| 41 | 41 |
\examples{
|
Catherine Ross authored on 03/11/2020 22:52:32 | ... | ... |
@@ -1,8 +1,8 @@ |
| 1 | 1 |
% Generated by roxygen2: do not edit by hand |
| 2 |
-% Please edit documentation in R/readPathways.R |
|
| 2 |
+% Please edit documentation in R/pathways.R |
|
| 3 | 3 |
\name{readPathways}
|
| 4 | 4 |
\alias{readPathways}
|
| 5 |
-\title{Returns a list of pathways from a file
|
|
| 5 |
+\title{Returns a list of pathways from a file.
|
|
| 6 | 6 |
Currently supports the following file format: GMT, TXT, XLSX} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| ... | ... |
@@ -35,7 +35,7 @@ use for non-GMT input (eg "Gene.ID", default = NULL)} |
| 35 | 35 |
a list of vectors with pathways |
| 36 | 36 |
} |
| 37 | 37 |
\description{
|
| 38 |
-Returns a list of pathways from a file |
|
| 38 |
+Returns a list of pathways from a file. |
|
| 39 | 39 |
Currently supports the following file format: GMT, TXT, XLSX |
| 40 | 40 |
} |
| 41 | 41 |
\examples{
|
Catherine Ross authored on 09/10/2020 20:45:05 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,49 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/readPathways.R |
|
| 3 |
+\name{readPathways}
|
|
| 4 |
+\alias{readPathways}
|
|
| 5 |
+\title{Returns a list of pathways from a file
|
|
| 6 |
+Currently supports the following file format: GMT, TXT, XLSX} |
|
| 7 |
+\usage{
|
|
| 8 |
+readPathways( |
|
| 9 |
+ pathway_file, |
|
| 10 |
+ header = TRUE, |
|
| 11 |
+ pathway_col, |
|
| 12 |
+ gene_col, |
|
| 13 |
+ MIN_GENE = 10L, |
|
| 14 |
+ MAX_GENE = 500L |
|
| 15 |
+) |
|
| 16 |
+} |
|
| 17 |
+\arguments{
|
|
| 18 |
+\item{pathway_file}{(char) path to file with pathway annotations}
|
|
| 19 |
+ |
|
| 20 |
+\item{header}{(logical) whether pathway_file has a header (default = TRUE)}
|
|
| 21 |
+ |
|
| 22 |
+\item{pathway_col}{(char) column name with pathway identifiers, one pathway per row
|
|
| 23 |
+use for non-GMT input (eg "Pathway.ID", default = NULL)} |
|
| 24 |
+ |
|
| 25 |
+\item{gene_col}{(char) column name with gene identifiers, one gene per row
|
|
| 26 |
+use for non-GMT input (eg "Gene.ID", default = NULL)} |
|
| 27 |
+ |
|
| 28 |
+\item{MIN_GENE}{(integer) minimum number of genes to be considered in a pathway
|
|
| 29 |
+(default = 10)} |
|
| 30 |
+ |
|
| 31 |
+\item{MAX_GENE}{(integer) maximum number of genes to be considered in a pathway
|
|
| 32 |
+(default = 500)} |
|
| 33 |
+} |
|
| 34 |
+\value{
|
|
| 35 |
+a list of vectors with pathways |
|
| 36 |
+} |
|
| 37 |
+\description{
|
|
| 38 |
+Returns a list of pathways from a file |
|
| 39 |
+Currently supports the following file format: GMT, TXT, XLSX |
|
| 40 |
+} |
|
| 41 |
+\examples{
|
|
| 42 |
+pathways <- readPathways( |
|
| 43 |
+ system.file("extdata", "YeastDatabase_GO_gmt.gmt", package = "FEDUP")
|
|
| 44 |
+) |
|
| 45 |
+pathways <- readPathways( |
|
| 46 |
+ system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),
|
|
| 47 |
+ header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "ORF.ID" |
|
| 48 |
+) |
|
| 49 |
+} |