streamline: Streamline

In Oshlack/Baller: Classification of RNA-seq data from ALL samples

Description

Produces a log FPKM (fragment/read per kilobase per million) of the genes necessary for classification. Requires a data frame of raw counts per gene (each row corresponds to a gene) and a vector of gene lengths. Note: in order to succesfully classify all twenty of the genes are required by the classifier.

Usage

streamline(counts,glengths)

Arguments

counts	A matrix of raw integer counts where each row is a gene and each column a different sample.
glengths	The length in bases of all genes (rows) in the counts matrix for which the FPKM is normalised to.

Value

A matrix of fragments/reads per kilobase per million. Rows are genes and columns are samples.

Examples

cf <- system.file("data","test_data.txt",package="AllSorts") #Get path to raw text file (a tsv)
counts <- read.table(file=cf,sep=' ',stringsAsFactors = FALSE,header=TRUE)
FPKM <- streamline(counts[,c(1:6)],counts$Gene_Length)

Oshlack/Baller documentation built on Jan. 23, 2021, 6:50 p.m.