gene expression data

Description Usage Arguments Details

Metrics include overlap between observed and expected signatures, JI between observed and expected signatures, and Fisher p value for selection of observed and expected signatures from a background set.

1 2	E3CompareSignatures(sampleGroups, group.signature = NULL, signature.ref = NULL, signature.expected = NULL, numgenes = 5000)

`sampleGroups`	- named list of character vectors. Each vector should represent a set of samples making up a group.
`group.signature`	- named list of character vectors. Each vector should represent the gene set (signature) associated with a group
`signature.ref`	- named character vector. Each element should link a sample name to a reference group, e.g. KO_ACTA_R1 would be linked to group KO_None
`signature.expected`	- named character vector. Each element should a sample to an expected signature group, e.g. KO_ACTA_R1 would be linked to group WT_ACTA
`numgenes`	- number of genes to use as background in calculation of Fisher metric.

Warning: the Fisher p value is computed very crudely using a background set of fixed size. This is in principle flawed, but the whole idea of using a Fisher test in such a scenario is flawed because not all genes are equally powered to be part of signatures. Bottom line is that the Fisher p values should be interpreted with care, they may be off even by two/three orders of magnitude.

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