runMBASED1s1aseID: Function that runs single-sample ASE calling using data from...

In MBASED: Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

Description

Function that runs single-sample ASE calling using data from loci (SNVs) within a single unit of ASE (gene). The i-th entry of each of vector arguments 'lociAllele1Counts', 'lociAllele2Counts', 'lociAllele1NoASEProbs', 'lociRhos' should correspond to the i-th locus. If argument 'isPhased' (see below) is true, then entries corresponding to allele1 at each locus must represent the same haplotype. Note: for each locus, at least one allele should have >0 supporting reads.

Usage

runMBASED1s1aseID(lociAllele1Counts, lociAllele2Counts, lociAllele1NoASEProbs,
  lociRhos, numSim = 0, isPhased = FALSE, tieBreakRandom = FALSE,
  checkArgs = FALSE)

Arguments

lociAllele1Counts,lociAllele2Counts	vectors of counts of allele1 (e.g. reference) and allele2 (e.g., alternative) at individual loci. Allele counts are not necessarily phased (see argument 'isPhased'), so allele1 counts may not represent the same haplotype. Both arguments must be vectors of non-negative integers.
lociAllele1NoASEProbs	probabilities of observing allele1-supporting reads at individual loci under conditions of no ASE (e.g., vector with all entries set to 0.5, if there is no pre-existing allelic bias at any locus). Must be a vector with entries >0 and <1.
lociRhos	dispersion parameters of beta distribution at individual loci (set to 0 if the read count-generating distribution at the locus is binomial). Must be a vector with entries >=0 and <1.
numSim	number of simulations to perform. Must be a non-negative integer. If 0 (DEFAULT), no simulations are performed.
isPhased	single boolean specifying whether the phasing has already been performed, in which case the lociAllele1Counts represent the same haplotype. DEFAULT: FALSE.
tieBreakRandom	single boolean specifying how ties should be broken during pseudo-phasing in cases of unphased data (isPhased=FALSE). If TRUE, each of the two allele will be assigned to major haplotype with probability=0.5. If FALSE (DEFAULT), allele1 will be assigned to major haplotype and allele2 to minor haplotype.
checkArgs	single boolean specifying whether arguments should be checked for adherence to specifications. DEFAULT: FALSE

Value

list with 6 elements

majorAlleleFrequency	Estimate of major allele frequency for this unit of ASE (gene).
pValueASE	Estimate of p-value for observed extent of ASE (nominal if no simulations are performed, simulations-based otherwise).
heterogeneityQ	Statistic summarizing variability of locus-specific estimates of major allele frequency if >1 locus is present. Set to NA for single-locus cases.
pValueHeterogeneity	Estimate of p-value for observed extent of variability of locus-specific estimates of major allele frequency if >1 locus is present. Set to NA for single-locus cases.
lociAllele1IsMajor	Vector of booleans, specifying for each locus whether allele1 is assigned to major (TRUE) or minor (FALSE) haplotype. If the data is phased (isPhased=TRUE), then all elements of the vector are TRUE if haplotype 1 is found to be major, and are all FALSE if haplotype 1 is found to be minor. In cases of unphased data (isPhased=FALSE), the assignment is provided by the pseudo-phasing procedure.
lociMAF	Estimate of major allele (haplotype) frequency at individual loci. Note that since 'major' and 'minor' distinction is made at the level of gene haplotype, there may be some loci where the frequency of the 'major' haplotype is <0.5.

Examples

SNVCoverage <- sample(10:100,5) ## gene with 5 loci
SNVAllele1Counts <- rbinom(length(SNVCoverage), SNVCoverage, 0.5)
MBASED:::runMBASED1s1aseID(lociAllele1Counts=SNVAllele1Counts, lociAllele2Counts=SNVCoverage-SNVAllele1Counts, lociAllele1NoASEProbs=rep(0.5, length(SNVCoverage)), lociRhos=rep(0, length(SNVCoverage)), numSim=0, isPhased=FALSE, tieBreakRandom=FALSE) ## data is not phased, no simulations
MBASED:::runMBASED1s1aseID(lociAllele1Counts=SNVAllele1Counts, lociAllele2Counts=SNVCoverage-SNVAllele1Counts, lociAllele1NoASEProbs=rep(0.5, length(SNVCoverage)), lociRhos=rep(0, length(SNVCoverage)), numSim=10^6, isPhased=FALSE, tieBreakRandom=FALSE) ## data is not phased, simulations
MBASED:::runMBASED1s1aseID(lociAllele1Counts=SNVAllele1Counts, lociAllele2Counts=SNVCoverage-SNVAllele1Counts, lociAllele1NoASEProbs=rep(0.5, length(SNVCoverage)), lociRhos=rep(0, length(SNVCoverage)),  numSim=0, isPhased=TRUE, tieBreakRandom=FALSE) ## data is phased, no simulations
MBASED:::runMBASED1s1aseID(lociAllele1Counts=SNVAllele1Counts, lociAllele2Counts=SNVCoverage-SNVAllele1Counts, lociAllele1NoASEProbs=rep(0.5, length(SNVCoverage)), lociRhos=rep(0, length(SNVCoverage)),  numSim=10^6, isPhased=TRUE, tieBreakRandom=FALSE) ## data is phased, simulations

MBASED documentation built on Nov. 8, 2020, 5:53 p.m.