E3CalcWithinGroupIntervalRescaleFactors: Estimates an interval rescale factor for each feature/gene...

Description Usage Arguments Details

Description

The goal is to find genes that are more variable in practice than the uncertainty interval model may suggest.

Usage

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E3CalcWithinGroupIntervalRescaleFactors(sampledata, id.col = "Gene",
  bg.samples = NULL, upper.quantile = 0.85, min.factor = 1)

Arguments

sampledata

- a list with tables $expression, $expression.low, $expression.high

id.col

- character strings. Name of column in sampledata that identifies the gene/transcript species

bg.samples

- list of sample names. Each vector should represent a group of related samples (replicates). The function will compute variability within each group.

upper.quantile

- numeric. The quantile used to equalize the input and output intervals.

min.factor

- numeric. Minimum rescaling factor, i.e. when procedure gives a suggestion to rescale by a factor lower than this, the output will in fact be min.factor.

Details

computes an empirical interval from values of a background sample set computes a representative interval from values of the background sample set computes the ratio of the empirical to representative - this is the output


tkonopka/ExpCube documentation built on May 31, 2019, 3:44 p.m.