limmaDiff-methods: limmaDiff

Description Usage Arguments

Description

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

Usage

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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/TPMaccess documentation built on Nov. 21, 2017, 10:19 a.m.