limmaDiff-methods: limmaDiff

In ericaenjoy3/RNA: RNA data analysis

Description

tpm.value either normalised to spikein or not filtering of genes must be done before hand

Usage

limmaDiff(obj, dout, pat, MA.it = TRUE, HEAT.it = TRUE, GO.it = TRUE,
  DiffOut.it = TRUE, logFCthresh = 1, PValthresh = NULL,
  PADJthresh = NULL, log2.it = TRUE, small = 0.05)

## S4 method for signature 'tpm'
limmaDiff(obj, dout, pat, MA.it = TRUE, HEAT.it = TRUE,
  GO.it = TRUE, DiffOut.it = TRUE, logFCthresh = 1, PValthresh = NULL,
  PADJthresh = NULL, log2.it = TRUE, small = 0.05)

Arguments

obj	A tpm object.
dout	A character string specifying the output directory.
pat	A character string specifying the prefix of file(s) without the directory name.
MA.it	A logical value indicating whether to generate an MA plot.
HEAT.it	A logical value specifying whether to draw a heatmap for each pairwise differnetially analysis.
GO.it	A logical value specifying whether to do gene ontology analysis.
DiffOut.it	A logical value specifying whether to write out differential analysis data to file.
logFCthresh	A numeric value specifying the log2 fold change threshold for data to be called differential.
PValthresh	A numeric value specifying the pvalue threshold for data to be called differential.
PADJthresh	A numeric value specifying the adjusted pvalue threshold for data to be called differential, overriding the specification of pvalue threshold.
log2.it	A logical value specifying whether to perform log2 transformation.
small	A numeric value indicating the adjustment to the TPM values before log2 transformation.

ericaenjoy3/RNA documentation built on May 28, 2019, 8:37 p.m.