BI_sametrend: find out genes that can be plot appropriately in boxplot with...

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

Description

find out genes that can be plot appropriately in boxplot with student test.

Usage

  sametrend(expr.matrix.list,
          res.list,
          logFC.col = "logFC",
          design,
          contrast="N.status",
          sigdif.co.id,
          count.test = T,
          log.convert = T,
          method="wilcox.test",
          p.cutoff = 0.05)

Arguments

expr.matrix.list	a list of different gene expression matrix.
res.list	a list of different results which contain logFC columns.
design	the design of gene expression matrix
contrast	the colname of design representing contrast.
sigdif.co.id	the range of test genes
logFC.col	the colnames of results
count.test	whether to make test like t test and so on.Always T.
log.convert	whether to make log scale in gene expression
method	method to do test

\itemp.cutoffcut-off of P value

Author(s)

Weibin Huang<[e-mail]>

Examples

## example
expr.matrix.list=list(test1 = expr,test2=expr)
res.list = list(test1 = sig.exprs,test2 = sig.exprs)
design = condition
contrast="condition"
sigdif.co.id = rownames(sig.exprs)
colnames(sig.exprs)
logFC.col = "logFC"
count.test =T
log.convert = F
method="wilcox.test"
p.cutoff=0.05
test1 <- sametrend(expr.matrix.list,
                   res.list,
                   logFC.col,
                   design,
                   contrast,
                   sigdif.co.id,
                   count.test,
                   log.convert,
                   method,
                   p.cutoff)

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