soft2exp.pval: expression matrix generator (with detection pvalue)

In htc502/ewrefxn: this package collects r fxns useful in my daily coding life

Description

given an accession number(gseXXXX), this fxn download and extract the expression matrix

Usage

soft2exp.pval(
  AccNum,
  detectp.col = 3,
  exp.col = 2,
  symbol.col,
  entrezID.col,
  phe.col,
  detectp = 0.05,
  detectionRate = 0.5,
  log2 = F
)

Arguments

AccNum	accession number
detectp.col	column number of detection p value
exp.col	column number of expression value
symbol.col	column number of expression value, for arraymatrix data the GPL header is usually SYMBOL; for agilent44K it is GENE_SYMBOL(10th column of GPL4134)
entrezID.col	column number of entrez id, for affymetrix data it is named Entrez_Gene_ID, for agilent it is GENE(9th column of GPL4134)
phe.col	specify the phenotype information want to extract from the gsmlist
detectionRate	threshold of sample detection rate for each gene
log2	set to T for logrithm transformation

Value

a list with expmatrix probeID symbols and entrezID

htc502/ewrefxn documentation built on Feb. 2, 2020, 9:14 a.m.