getControls: Get a set of genes that can be used to differentiate between...

In roonysgalbi/tispec: Calculates tissue specificity from RNA-seq data

Description

This function selects 2 lists of genes, 1 for each tissue. Each list includes genes that are highly specific and expressed in one tissue with <0.1 quantile normalised expression in the other. This is useful for differentiating between tissue types. For example, for selecting positive & negative controls for qPCR to determine if a tissue sample has been contaminated.

Usage

getControls(x, y)

Arguments

x	primary tissue, output from getTissue()
y	secondary tissue, output from getTissue()

Value

Returns a list object containing 1 dataframe of genes for each of the 2 tissues. The data frames are ranked first by score and then by quantile normalised expression

Examples

# Usage
controls <- getControls(tissueA, tissueB)
# To confirm the difference in expression between tissues
x <- rownames(head(controls$tissueA, n = 1))
qnExp[x, ]
tissueA[x, ]
tissueB[x, ]

roonysgalbi/tispec documentation built on May 26, 2019, 1:33 a.m.