getTissue: Get expression and specificity of each gene in a single...

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

Description

This function takes a user defined tissue and extracts the ensembl annotations, normalised expression values, tau values, and tau expression fractions of all genes in that tissue. Each gene's score is the sum of it's tau expression fraction value and it's 0-1 ranged normalised expression value. The gene with the greatest expression and highest specificity recieves the highest score.

Usage

getTissue(x, y, z)

Arguments

x	tissue of interest (case sensitive)
y	output from quantNorm()
z	output from getMart()

Value

Returns a data frame of ensembl annotations, normalised expression and specificity values

Examples

x <- head(colnames(meanExp), n = 1)
x <- getTissue(x, qnExp, tauAnno)
head(x)
y <- rownames(head(x, n = 1))
qnExp[y,]
tauAnno[y,]

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