edger_confects: Confident log2 fold change based on the edgeR...

Description Usage Arguments Details Value

View source: R/edger.R

Description

For all possible absolute log2 fold changes (LFC), which genes have at least this fold change at a specified False Discovery Rate?

Usage

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edger_confects(fit, coef = NULL, contrast = NULL, fdr = 0.05,
  step = 0.01, null = "worst.case")

Arguments

fit

An edgeR DGEGLM object produced using glmQLFit.

coef

Coefficient to test, as per glmTreat. Use either coef or contrast or effect.

contrast

Contrast to test, as per glmTreat. Use either coef or contrast or effect.

fdr

False Discovery Rate to control for.

step

Granularity of log2 fold changes to test.

null

"null" parameter passed through to edger::glmTreat (if coef or contrast given). Choices are "worst.case" or "interval". Note that the default here is "worst.case", to be consistent with other functions in topconfects. This differs from the default for glmTreat.

Details

Results are presented in a table such that for any given LFC, if the reader chooses the genes with abs(confect) less than this they are assured that this set of genes has at least this LFC (with the specified FDR). The confect column may also be viewed as a confidence bound on the LFC of each gene, with a dynamic correction for multiple testing.

Value

See nest_confects for details of how to interpret the result.


pfh/topconfects documentation built on July 2, 2018, 6:31 a.m.