jaguar_slice: Slice gene expression data into multiple partitions

In cramanuj/JAGUAR: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)

Description

Function to 1) create sub-directories, 2) slice gene expression data into partitions of predetermined size, and 3) sliced gene expression partitions are deposited into each sub-directory

Usage

jaguar_slice(geneexp,size,path=getwd())

Arguments

geneexp	A matrix of gene expression data with gene on rows and patient samples on columns. There has to be equal number of samples in each group. Samples (columns in the geneexp object) with missing gene expression values for any group/tissue MUST be included in the data
size	Integer indicating the size of each slice of gene expression data.
path	Location for the sub-directories. Please give the full path. Default is set to the current directory.

Author(s)

Chaitanya R. Acharya Maintainer: Chaitanya Acharya<[e-mail]>

References

Chaitanya R. Acharya, Kouros Owzar, Janice M. McCarthy and Andrew S. Allen; Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. BMC Bioinformatics (2016) 17:257 DOI 10.1186/s12859-016-1123-5

See Also

jaguar_gwa,jaguar_process,jaguar_sim,jaguar_plotqtl,jaguar_cis

Examples

# Set the size of the partition
# size = 100; ## Indicates the number of genes in each partitioned gene exp data
#
# Assuming that the path is the default getwd()
# jaguar_slice(geneexp,size)

cramanuj/JAGUAR documentation built on May 13, 2019, 10:55 p.m.