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GSEABase feaetures

Pourya Naderi authored on 07/01/2022 03:27:44
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@@ -4,7 +4,13 @@
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 \alias{pathwayGeneTab}
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 \title{Pathway-Gene Associations}
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 \usage{
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-pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA)
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+pathwayGeneTab(
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+  pathAdress = NA,
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+  pathwayList = NA,
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+  fromType = "ENTREZID",
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+  toType = "ENSEMBL",
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+  outDir = NA
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+)
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 }
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 \arguments{
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 \item{pathAdress}{Address to an RDS file containing list of pathways where
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@@ -13,6 +19,10 @@ each element is a list of genes similar to GMT format.}
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 \item{pathwayList}{If you wish to use a list of pathways instead of a file
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 use this argument instead. The list must contain no NA values.}
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+\item{fromType}{gene annotation type used in your input data.}
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+
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+\item{toType}{gene annotation type to be produced in the output.}
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+
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 \item{outDir}{Address to save an RDS for a table of pathway-gene association}
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 }
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 \value{
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BiocCheck progress

Pourya Naderi authored on 01/12/2021 20:24:29
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@@ -21,3 +21,12 @@ pathExpTab Table of pathway-gene association.
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 \description{
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 Generates a table of pathways and genes associations.
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 }
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+\examples{
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+pathway1 <- c("125", "3099", "126")
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+pathway2 <- c("5232", "5230", "5162")
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+pathList <- list("Path1" = pathway1, "Path2" = pathway2)
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+res <- pathwayGeneTab(pathwayList = pathList)
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+
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+data(msigdb_c2)
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+pathwayGeneTab(pathwayList = msigdb_c2[1:2])
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+}
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Rd update

Pourya Naderi authored on 01/12/2021 15:17:16
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/utils.R
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+\name{pathwayGeneTab}
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+\alias{pathwayGeneTab}
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+\title{Pathway-Gene Associations}
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+\usage{
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+pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA)
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+}
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+\arguments{
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+\item{pathAdress}{Address to an RDS file containing list of pathways where
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+each element is a list of genes similar to GMT format.}
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+
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+\item{pathwayList}{If you wish to use a list of pathways instead of a file
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+use this argument instead. The list must contain no NA values.}
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+
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+\item{outDir}{Address to save an RDS for a table of pathway-gene association}
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+}
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+\value{
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+pathExpTab Table of pathway-gene association.
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+}
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+\description{
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+Generates a table of pathways and genes associations.
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+}
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Rd problems

Pourya Naderi authored on 01/12/2021 15:16:55
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deleted file mode 100644
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@@ -1,23 +0,0 @@
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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/utils.R
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-\name{pathwayGeneTab}
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-\alias{pathwayGeneTab}
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-\title{Pathway-Gene Associations}
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-\usage{
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-pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA)
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-}
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-\arguments{
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-\item{pathAdress}{Address to an RDS file containing list of pathways where
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-each element is a list of genes similar to GMT format.}
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-
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-\item{pathwayList}{If you wish to use a list of pathways instead of a file
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-use this argument instead. The list must contain no NA values.}
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-
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-\item{outDir}{Address to save an RDS for a table of pathway-gene association}
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-}
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-\value{
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-pathExpTab Table of pathway-gene association.
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-}
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-\description{
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-Generates a table of pathways and genes associations.
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-}
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camelCaps utils, clean up

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Pourya Naderi authored on 18/11/2021 17:33:22
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@@ -4,16 +4,16 @@
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 \alias{pathwayGeneTab}
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 \title{Pathway-Gene Associations}
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 \usage{
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-pathwayGeneTab(path.address = NA, pathway.list = NA, out.dir = NA)
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+pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA)
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 }
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 \arguments{
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-\item{path.address}{Address to an RDS file containing list of pathways where
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+\item{pathAdress}{Address to an RDS file containing list of pathways where
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 each element is a list of genes similar to GMT format.}
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-\item{pathway.list}{If you wish to use a list of pathways instead of a file
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+\item{pathwayList}{If you wish to use a list of pathways instead of a file
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 use this argument instead. The list must contain no NA values.}
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-\item{out.dir}{Address to save an RDS for a table of pathway-gene association}
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+\item{outDir}{Address to save an RDS for a table of pathway-gene association}
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 }
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 \value{
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 pathExpTab Table of pathway-gene association.
Browse code

camelCaps 04

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Pourya Naderi authored on 18/11/2021 16:00:50
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@@ -0,0 +1,23 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/utils.R
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+\name{pathwayGeneTab}
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+\alias{pathwayGeneTab}
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+\title{Pathway-Gene Associations}
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+\usage{
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+pathwayGeneTab(path.address = NA, pathway.list = NA, out.dir = NA)
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+}
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+\arguments{
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+\item{path.address}{Address to an RDS file containing list of pathways where
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+each element is a list of genes similar to GMT format.}
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+
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+\item{pathway.list}{If you wish to use a list of pathways instead of a file
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+use this argument instead. The list must contain no NA values.}
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+
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+\item{out.dir}{Address to save an RDS for a table of pathway-gene association}
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+}
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+\value{
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+pathExpTab Table of pathway-gene association.
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+}
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+\description{
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+Generates a table of pathways and genes associations.
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+}