Description Usage Arguments Value Author(s) References Examples
View source: R/coreTDT_geneset.R
This program is used to compute the pvalues for Transimission Disequilibrium Test for compound heterozygous and recessive models
1 2 3 4 5 6 | coreTDT_geneset(samplePed, controlInf, useControlMAF = TRUE, maf.threshold = 1,
qc.proportion = 0.8, geneList = c(),
outputFile = "coreTDT_analysis.out",
chrX = FALSE,writeFile=FALSE)
coreTDT_single(ped, maf.threshold = 1, qc.proportion = 0.8,
geneid = NA,control.maf = NULL)
|
samplePed |
plink file to input genetype informations, ref to PLINK recodeA |
controlInf |
Files form ATAV,contain information about variants,(evs dataset used) |
useControlMAF |
logical, if true, remove the variants with control MAF >= maf.threshold, else use parents MAF |
maf.threshold |
The allowed maximum of MAF that variants will be used in computation |
qc.proportion |
variants that have more than qc.proportion families with enough coverage will be used in computation |
geneList |
a vector containing gene names that used to analysis |
outputFile |
output file name |
chrX |
logical, if true, analyse chromosome X, not activated yet |
writeFile |
logical, if true, write the results to outputFile |
ped |
contain the genotype information for all samples,assume m families and n snps, 3m * n matrix, each column represents a variant, coded by 0/1/2 (number of alternative alleles);each row represents a sample, the first m rows are for child,the second m rows are for mother,the last m rows are for father |
geneid |
character, gene name |
control.maf |
vector contain the MAF of each variant in controls |
pvalue_pr |
pvalues computed from probabaility model |
pvalue_lr |
pvalues from likelihood ratio test with restricted alternative hypothesis |
pvalue_lr2 |
pvalues from likelihood ratio test |
nmissing |
number of variants is missing in data |
nMedErr |
number of loci contain mendel errors |
nfamily |
sample size |
nsnp |
number of variants used in analysis |
N11 |
number of family with parents compound genotype 1,1 |
N12 |
number of family with parents compound genotype 1,2 |
N112 |
number of family with compound genotype 1,1,2 |
N122 |
number of family with compound genotype 1,2,2 |
Yu Jiang, Andrew S. Allen Maintainer: Yu Jiang <yu.jiang@dm.duke.edu>
Yu Jiang, Janice M McCarthy, Andrew S Allen,Testing the effect of rare compound-heterozygous and recessive mutations in case-parent sequencing studies (In Preparation)
1 2 3 | data(coreTDTexample)
attach(coreTDTexample)
coreTDT_geneset(samplePed, controlInf,maf.threshold=0.05,writeFile=FALSE)
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