epimethex.analysis: Create a Epimethex function

In giupardeb/EpiMethEx: EpiMethEx Package

Description

Create a Epimethex function

Usage

epimethex.analysis(dfExpressions, dfGpl, dfMethylation, minRangeGene,
    maxRangeGene, numCores, dataGenesLinear, testExpression, testMethylation)

Arguments

dfExpressions	data frame, expression of data
dfGpl	data frame, Annotations of data
dfMethylation	data frame, Methylation of data
minRangeGene	Numeric, lowerbound of genes
maxRangeGene	Numeric, upperbound of genes
numCores	Numeric, is the number of cores that you can use
dataGenesLinear	Logic, determines if genetic data are linear
testExpression	Logic, determines the test to apply on expression dataset. If TRUE will apply t-student test, otherwise will apply Kolmogorov-Smirnov test
testMethylation	Logic, determines the test to apply on methylation dataset. If TRUE will apply t-student test, otherwise will apply Kolmogorov-Smirnov test

Value

csv files

Source

Functions

Examples

Annotations <- data.frame(
ID = c("cg11663302","cg01552731", "cg09081385"),
Relation_to_UCSC_CpG_Island = c("Island","N_Shore","N_Shore"),
UCSC_CpG_Islands_Name = c("chr1:18023481-18023792","chr19:46806998-46807617",
"chr12:120972167-120972447"),
UCSC_RefGene_Accession = c("NM_001011722","NM_152794","NM_014868"),
Chromosome_36 = c("1","19","12"),
Coordinate_36 = c("17896255","51498747","119456453"),
UCSC_RefGene_Name = c("ARHGEF10L","HIF3A","RNF10"),
UCSC_RefGene_Group =c("Body","1stExon","TSS200"),
stringsAsFactors=FALSE)

Expressions <- data.frame(
'sample' = c("ARHGEF10L", "HIF3A", "RNF10"),
'TCGA-YD-A89C-06' = c(-0.746592469762, -0.753826336325, 0.4953280),
'TCGA-Z2-AA3V-06' = c(0.578807530238, -2.30662633632, 0.1023280),
'TCGA-EB-A3Y6-01' = c(-0.363492469762, -2.67922633632, -0.6147720),
'TCGA-EE-A3JA-06' = c(-2.97279246976, -3.61932633632, 0.02932801),
'TCGA-D9-A4Z2-01' = c(-0.128492469762, 0.679073663675, 0.4017280),
'TCGA-D3-A51G-06' = c(-0.4299925, -4.0626263, -1.0136720),
stringsAsFactors=FALSE)

Methylation <- data.frame(
'sample' = c("cg11663302", "cg01552731", "cg09081385"),
'TCGA-YD-A89C-06' = c(0.9856, 0.7681, 0.0407),
'TCGA-Z2-AA3V-06' = c(0.9863, 0.8551, 0.0244),
'TCGA-EB-A3Y6-01' = c(0.9876, 0.6473, 0.028),
'TCGA-EE-A3JA-06' = c(0.9826, 0.4587, 0.0343),
'TCGA-D9-A4Z2-01' = c(0.9881, 0.8509, 0.0215),
'TCGA-D3-A51G-06' = c(0.9774, 0.813, 0.0332),
stringsAsFactors=FALSE)

epimethex.analysis(Expressions, Annotations, Methylation, 1, 3, 2,
TRUE, TRUE, FALSE)

giupardeb/EpiMethEx documentation built on May 28, 2019, 5:39 a.m.