GRangesFromExClustResults: Converts ExCluster results data table to GRanges format.

In RMTbioinfo/ExCluster: ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

Description

GRangesFromExClustResults converts the results from the main ExCluster function into GRanges objects using the GRanges package.

Usage

GRangesFromExClustResults(results.ExClust)

Arguments

results.ExClust

This argument should be given the table of data that the main ExCluster function produces. This table of data should contain at minimum 12 columns, plus exin bin read count columns if they are present.

Value

This function returns a GRanges object with ExCluster main function results, in the form of a table of data.

Author(s)

R. Matthew Tanner

References

Lawrence M, Huber W, Pag\'es H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118.doi:10.1371/journal.pcbi.1003118

Examples

# grab the path to the sub-sampled ExCluster toy dataset results from the ExCluster function
ExClust_Results <- system.file("extdata","sub_ExClust_results.txt",package="ExCluster")
# read this data into R
ExClust_Results <- read.table(file=ExClust_Results, sep="\t",header=TRUE,stringsAsFactors=FALSE)
# run the GRangesFromExClustResults function
GRanges.ExClustResults <- GRangesFromExClustResults(results.ExClust=ExClust_Results)

RMTbioinfo/ExCluster documentation built on May 15, 2019, 3:14 p.m.