mglR (version 0.1.0)

makeCoXpTranscript: Tests pairwise co-expression between user defined transcripts in specified tissues

Description

makeCoXpTranscript returns a list of cor.test output for each transcript pair in a given tissue

Usage

makeCoXpTranscript(mgl, transcripts = c(), genes = c(), data = c(9, 11), makePlot = FALSE, saveFile = FALSE, tissue = c("All", "Adipose - Subcutaneous", "Adipose - Visceral (Omentum)", "Adrenal Gland", "Artery - Aorta", "Artery - Coronary", "Artery - Tibial", "Bladder", "Brain - Amygdala", "Brain - Anterior cingulate cortex (BA24)", "Brain - Caudate (basal ganglia)", "Brain - Cerebellar Hemisphere", "Brain - Cerebellum", "Brain - Cortex", "Brain - Frontal Cortex (BA9)", "Brain - Hippocampus", "Brain - Hypothalamus", "Brain - Nucleus accumbens (basal ganglia)", "Brain - Putamen (basal ganglia)", "Brain - Spinal cord (cervical c-1)",      "Brain - Substantia nigra", "Breast - Mammary Tissue", "Cells - EBV-transformed lymphocytes", "Cells - Transformed fibroblasts", "Cervix - Ectocervix", "Cervix - Endocervix", "Colon - Sigmoid", "Colon - Transverse", "Esophagus - Gastroesophageal Junction", "Esophagus - Mucosa", "Esophagus - Muscularis", "Fallopian Tube", "Heart - Atrial Appendage", "Heart - Left Ventricle", "Kidney - Cortex", "Liver", "Lung", "Minor Salivary Gland", "Muscle - Skeletal", "Nerve - Tibial", "Ovary", "Pancreas",      "Pituitary", "Prostate", "Skin - Not Sun Exposed (Suprapubic)", "Skin - Sun Exposed (Lower leg)", "Small Intestine - Terminal Ileum", "Spleen", "Stomach", "Testis", "Thyroid", "Uterus", "Vagina", "Whole Blood"))

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

transcripts

Character vector indicating transcripts to be considered (see mgl[[x]][[2]] where x is number corresponding to gene of interest)

genes

Character vector indicating genes corresponding to transcripts to be considered (note gene names must match names(mgl))

data

Number corresponding to element of mgl containing data of interest: 8 for count data and 10 for RPKM

makePlot

A logical flag indicating whether a pdf file ('CoXpGene.pdf') should be saved in the current directory

saveFile

A logical flag indicating whether a csv file ('CoXpGene.csv') should be saved in the current directory. 'CoXpGene.csv' contains cor.test results

tissue

Character vector indicating tissues to be considered (note tissue names must match those provided here: c('All', 'Adipose - Subcutaneous', 'Adipose - Visceral (Omentum)', 'Adrenal Gland', 'Artery - Aorta', 'Artery - Coronary', 'Artery - Tibial', 'Bladder', 'Brain - Amygdala', 'Brain - Anterior cingulate cortex (BA24)', 'Brain - Caudate (basal ganglia)', 'Brain - Cerebellar Hemisphere', 'Brain - Cerebellum', 'Brain - Cortex', 'Brain - Frontal Cortex (BA9)', 'Brain - Hippocampus', 'Brain - Hypothalamus', 'Brain - Nucleus accumbens (basal ganglia)', 'Brain - Putamen (basal ganglia)', 'Brain - Spinal cord (cervical c-1)', 'Brain - Substantia nigra', 'Breast - Mammary Tissue', 'Cells - EBV-transformed lymphocytes', 'Cells - Transformed fibroblasts', 'Cervix - Ectocervix', 'Cervix - Endocervix', 'Colon - Sigmoid', 'Colon - Transverse', 'Esophagus - Gastroesophageal Junction', 'Esophagus - Mucosa', 'Esophagus - Muscularis', 'Fallopian Tube', 'Heart - Atrial Appendage', 'Heart - Left Ventricle', 'Kidney - Cortex', 'Liver', 'Lung', 'Minor Salivary Gland', 'Muscle - Skeletal', 'Nerve - Tibial', 'Ovary', 'Pancreas', 'Pituitary', 'Prostate', 'Skin - Not Sun Exposed (Suprapubic)', 'Skin - Sun Exposed (Lower leg)', 'Small Intestine - Terminal Ileum', 'Spleen', 'Stomach', 'Testis', 'Thyroid', 'Uterus', 'Vagina', 'Whole Blood'))

Details

Uses the cor.test function in R to test for co-expression between transcripts. Option to generate scatter plots and a summary table of the correlations to be saved as a pdf and csv, respectively. Any number of transcripts and tissues can be included. Counts (data = 9) or RPKM (data = 11) can be used.

See Also

Other output: makeAeiPlot, makeCoXpGene, makeDnaseSig, makeGoSearch, makeGo, makeMultiEqtl, makeOverlapTable, makeOverlap, makePhenotypeSearch, makePhenotypes, makeSnpSearch, makeSnps, makeSummary

Examples

exMgl() -> myMgl
makeCoXpTranscript(myMgl, transcripts = 
    c('ENST00000344348', 'ENST00000414907', 'ENST00000478719'), 
    genes = c('NCOA4', 'NCOA4', 'MSMB'), tissue = c('Prostate'), 
    data = 9, makePlot = FALSE, saveFile = FALSE)