getOptimum: Extract a set of genes that are both highly specific for and...

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

Description

This function ranks genes by their score (as calculated in getTissue()) and extracts the highest scoring genes that are highly specific to the tissue of interest (>=0.85 tau expression fraction). The number of genes extracted is defined by the user (z). This function is ideal for selecting a gene set that has little expression outside the tissue of interest, while also enough expression in the tissue of interest to facilitate bench work in the laboratory.

Usage

getOptimum(x, y, z)

Arguments

x	output from getMart()
y	output from getTissue()
z	number of genes

Value

Returns a list of 2 objects: a dataframe and a ggplot barplot. The dataframe is a subset of the output of getTissue(), containing only the optimum gene set. The barplot shows only the tissues in which the optimum genes are expressed and the specificity of those genes for those tissues. Red dotted line: 0.85 tau expression fraction threshold for high tissue specificity

Examples

optimum <- getOptimum(tauAnno, tissueA, 5)
optimum$dataframe
optimum$barplot

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