gene expression data

Description Usage Arguments

Function returns a list with two tables. Values in one table are expected fold changes. Values in the other tables are observed fold changes. See descriptions of arguments to see how these are computed. Each table will have gene names in rownames and group names in colnames.

1 2	E3GetObservedExpectedGroupFC(sampleexp, sampleGroups, signature.ref, signature.expected, fun = mean, add.dark = 1, id.col = "Gene")

`sampleexp`	- data frame with columns (Gene, SAMPLENAMES)
`sampleGroups`	- named list of character vectors (sample names). Names indicate sample grouping, e.g. group WT_None3 containing samples c("WT_None3_R1", "WT_None2_R2")
`signature.ref`	- named character vector. This should link samplenames to a group with reference samples, e.g. sample KO_ACTA_R1 will link to a reference group KO_None.
`signature.expected`	- names character vector. This should link samplenames to expected signature groups, e.g. sample KO_ACTA_R1 will be expected to be similar to group WT_ACTA.
`fun`	- function. Used to summarize data from multiple samples into one group value. The mean summary function is usually appropriate and fast.
`add.dark`	- numeric. a dark count for the expression values. This is useful to avoid division by zeros.
`id.col`	- name of column in sampleexp with gene identifier