Browse code

minor changes to example comments

catherine authored on 24/04/2021 22:14:36
Showing1 changed files
... ...
@@ -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"
Browse code

updated docs

Catherine Ross authored on 23/03/2021 23:37:33
Showing1 changed files
... ...
@@ -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(
Browse code

formatting line spaces

Catherine Ross authored on 05/03/2021 23:01:00
Showing1 changed files
... ...
@@ -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{
Browse code

renaming project

Catherine Ross authored on 21/02/2021 05:36:05
Showing1 changed files
... ...
@@ -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
 }
Browse code

support for pathCol (formerly pathwayCol) and geneCol to accept column numbers or column names as input

Catherine Ross authored on 18/02/2021 20:45:03
Showing1 changed files
... ...
@@ -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
 }
Browse code

biocthis::bioc_style() changes

Catherine Ross authored on 12/02/2021 21:24:28
Showing1 changed files
... ...
@@ -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
 }
Browse code

following bioc coding style (camelCaps, spaces using named arguments to functions)

Catherine Ross authored on 12/02/2021 06:50:44
Showing1 changed files
... ...
@@ -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
 }
Browse code

README updates

Former-commit-id: 4d51792bca083f02938e7375225eff324d219c86

Catherine Ross authored on 11/02/2021 07:27:35
Showing1 changed files
... ...
@@ -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.
Browse code

Merge branch 'main' of https://github.com/rosscm/FEDUP into main

Former-commit-id: 603e9281202cf5a276c7c1a612264fd350efa501

Catherine Ross authored on 11/02/2021 07:21:45
Showing0 changed files
Browse code

removed GO_class param from param list but not the actual function, so good

Former-commit-id: 3fc088bec88f63f8dbe1c83f960586edc2cb3d00

Catherine Ross authored on 11/02/2021 07:18:35
Showing1 changed files
... ...
@@ -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.
Browse code

man page updates

Former-commit-id: 04af82691b9ada33877c0ff4d1ee4455e520ee11

Catherine Ross authored on 10/02/2021 07:10:06
Showing1 changed files
... ...
@@ -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
 }
Browse code

man page updates

Former-commit-id: 6c9cb5c25c50990937f6f4fad54168326755e9ee

Catherine Ross authored on 10/02/2021 07:10:06
Showing1 changed files
... ...
@@ -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
 }
Browse code

man file updates

Former-commit-id: 8963930bbc9b73fe0e3785708d466695c5144f93

Catherine Ross authored on 05/02/2021 23:28:08
Showing1 changed files
... ...
@@ -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
 }
Browse code

man file updates

Former-commit-id: 6f876229b0af1113b79d5b357b6378af7c95222f

Catherine Ross authored on 05/02/2021 23:28:08
Showing1 changed files
... ...
@@ -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
 }
Browse code

roxygen generated files

Former-commit-id: f10b80ebf948d722a8773104b6d6bc41e7a2644b

Catherine Ross authored on 29/01/2021 23:17:47
Showing1 changed files
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
+}
Browse code

roxygen generated files

Former-commit-id: 0ef905fee4bf648953d9a4f6dcb3a09a07a09abd

Catherine Ross authored on 29/01/2021 23:17:47
Showing1 changed files
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
+}
Browse code

roxygen function man

Catherine Ross authored on 20/11/2020 21:42:53
Showing1 changed files
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
-}
Browse code

roxygen function man

Catherine Ross authored on 20/11/2020 21:42:53
Showing1 changed files
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
-}
Browse code

documenting data sets

Catherine Ross authored on 03/11/2020 22:52:32
Showing1 changed files
... ...
@@ -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{
Browse code

documenting data sets

Catherine Ross authored on 03/11/2020 22:52:32
Showing1 changed files
... ...
@@ -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{
Browse code

roxygen documents

Catherine Ross authored on 09/10/2020 20:45:05
Showing1 changed files
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
+}