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Last data update: 2014.03.03

R: Slice gene expression data into multiple partitions

jaguar_slice

R Documentation

Slice gene expression data into multiple partitions

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, Andrew S. Allen Maintainer: Chaitanya Acharya<c.acharya@duke.edu>

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 (Manuscript submitted)

Chaitanya R. Acharya and Andrew S. Allen; JAGUAR: An R-package to Implement Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test to Map eQTL (Manuscript submitted)

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(JAGUAR)
Loading required package: Rcpp
Loading required package: plyr
Loading required package: lme4
Loading required package: Matrix
Loading required package: reshape2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/JAGUAR/jaguar_slice.Rd_%03d_medium.png", width=480, height=480)
> ### Name: jaguar_slice
> ### Title: Slice gene expression data into multiple partitions
> ### Aliases: jaguar_slice
> ### Keywords: partition slice gene expression sub-directory
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>