E3GetDEScores: Compute DE scores for a single sample.

Description Usage Arguments

Description

Function returns a named vector with scores [-1,1]. Names are genes. Values are scores that indicate whether a gene is DE based on FC and z criteria.

Usage

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E3GetDEScores(sampledata, sampleA, refsamples, scorefun = E3DEscore,
  rankrescale = TRUE, shiftval = 0.1)

Arguments

sampledata

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

sampleA

- character string. The sample for which the signature is made

refsamples

- character vector. Reference samples to which sampleA is compared.

scorefun

- function. This function should accept two arguments (fc and z) and return a numeric score.

rankrescale

- logical. Set TRUE to penalize scores in an ad-hoc way for genes that have a high score but lower fc or lower z than many other genes.

shiftval

- numeric. Used when computing FC to avoid division by zero. return - a vector with gene names and then a score [0,1] Score 1 means the gene is DE wrt all samples in groupB


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