tmodLimmaTopTable: tmod's replacement for the limma topTable function

Description Usage Arguments Details Value See Also

View source: R/limma.R

Description

Produce a data frame for all or for selected coefficients of a linear fit object, including log fold changes, q-values, confidence intervals and MSD.

Usage

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tmodLimmaTopTable(f, genelist = NULL, coef = NULL, adjust.method = "BH",
  confint = 0.95)

Arguments

f

result of linear model fit produced by limma functions lmFit and eBayes

genelist

A data frame or a character vector with additional information on the genes / probes

coef

Which coefficients to extract

adjust.method

Which method of p-value adjustment; see "p.adjust()"

confint

Confidence interval to be calculated

Details

Produce a data frame for all or for selected coefficients of a linear fit object, including log fold changes, q-values, confidence intervals and MSD. For each coefficient, these four columns will be created in the output file, with the name consisting of a prefix indicating the type of the column ("msd", "logFC", "qval", "SE", "ci.L", "ci.R") and the name of the coefficient.

Value

A data frame with all genes.

See Also

tmodLimmaTest


tmod documentation built on March 18, 2018, 1:59 p.m.