BI_getexpr: get long data frame from a gene expression matrix.

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

getexpr help get long data frame from a gene expression matrix.

Usage

getexpr(exprs.matirx,
        design,
        select,
        contrast.col,
        contrast.list=NULL)

Arguments

exprs.matirx	genes expression matrix or a matrix with individual colnames and marker rownames.
design	design object
select	selected markers or genes
contrast.col	the colnames of the contrast
contrast.list	the elements of a contrast like Np and N0. If NULL,use all the contrast element.

Author(s)

Weibin Huang

Examples

data(expr)
exprs.matirx <- expr[,1:(ncol(expr)-3)]
design=data.frame(condition=Fastextra(colnames(exprs.matirx),"_",2))
select = c("gene1","gene2","gene3","gene4","gene5","gene6")
contrast.col = "condition"
contrast.list = as.character(unique(design$condition))

df1 <- getexpr(exprs.matirx,
               design,
               select,
               contrast.col,
               contrast.list=NULL)

df2 <- getexpr(exprs.matirx,
               design,
               select,
               contrast.col,
               contrast.list)

df3 <- getexpr(exprs.matirx,
               design,
               select,
               contrast.col,
               contrast.list=contrast.list[1:2])

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.