processData: Create X Y linked SNP's allelic expression

In cavei/guessMyLOI: Guess Loss Of Imprinting

Description

Create X Y linked SNP's allelic expression

Create Non Sexual linked SNP's allelic expression

Usage

processSexualData(gatk_ai, countsToCall, total, callheteroThr,
  species = c("hsapien", "mmusculus"), removeNonDBsnp = TRUE)

processNonSexualData(gatk_ai, countsToCall, total, callheteroThr,
  species = c("hsapien", "mmusculus"), removeNonDBsnp = TRUE)

Arguments

gatk_ai	allelic imbalance from readGATK.AllelicImbalance
countsToCall	how many counts to the alternative allele to call
total	use tota as denominator in the allele ratios
callheteroThr	the threshold to call hetorozygous
species	either hsapiens or mmusculus. Choose the species to remove pseudoAutosomal regions
removeNonDBsnp	should I remove the non DBsnp SNPs

Value

a list with

genes	genes related object for visualization
snps	snps related object for visualization
geneSummary	tabular summary of the genes
snpSummary	tabular summary of the SNPs

cavei/guessMyLOI documentation built on May 24, 2019, 7:14 a.m.