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Last data update: 2014.03.03

R: newIdMatrix

newIdMatrix

R Documentation

newIdMatrix

Description

A function to convert ID.

Usage

newIdMatrix(x, convertIdTable, genesKept = c("var", "foldchange", "abs",
  "first", "random"))

Arguments

`x`	the expression data matrix.
`convertIdTable`	A vector. The names should be the source IDs, and the values should be the target IDs.
`genesKept`	The method to select target gene in more than one targets. "var"/"foldchange"/"abs" means selecting the gene with largest variation/fold change/absolute value. "first" means selecting the first target and "random" means randomly selection.

Details

A function to convert ID.

Examples

convertIdTable<-paste("New",c(1,2,2,2,1,3,4,4,5,5))
names(convertIdTable)<-paste("Old",1:length(convertIdTable))
temp<-matrix(rnorm(20),ncol=2)
row.names(temp)<-names(convertIdTable)
colnames(temp)<-c("Exp1","Exp2")
newIdMatrix(temp,genesKept="foldchange",convertIdTable)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(KEGGprofile)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGprofile/newIdMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: newIdMatrix
> ### Title: newIdMatrix
> ### Aliases: newIdMatrix
> 
> ### ** Examples
> 
> convertIdTable<-paste("New",c(1,2,2,2,1,3,4,4,5,5))
> names(convertIdTable)<-paste("Old",1:length(convertIdTable))
> temp<-matrix(rnorm(20),ncol=2)
> row.names(temp)<-names(convertIdTable)
> colnames(temp)<-c("Exp1","Exp2")
> newIdMatrix(temp,genesKept="foldchange",convertIdTable)
            Exp1       Exp2
New 1  0.3689399  2.1048044
New 2 -2.2420981  0.2071265
New 3 -0.1770710  1.6386308
New 4  0.1119039 -1.5215000
New 5 -1.5513755 -0.7464663
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>