calculateLDSNPandCNV: calculateLDSNPandCNV

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Description

Identifying SNPs/INDELs being in linkage disequilibrium with CNV.

Usage

calculateLDSNPandCNV(sampleCNV = NULL, vcfFile = NULL,
	matrixGenotype = NULL, cnvColumn = NULL, popColumn = NULL,
	population = NULL, chr = NULL, hg = "hg19", 
	st = NULL, en = NULL,	nChunkForVcf = 10, 
	codeSNP = c("Two", "Three"), codeCNV = c("CN", "ThreeGroup"),
	typeTest = c("All", "Dup", "Del"), parallel = FALSE)

Arguments

sampleCNV	A data frame with no missing data; The first column is samples, the other columns are copy number, population names. This object can be obtained from the clustering step (allGroups).
vcfFile	Name of zipped vcf file including SNPs/INDELs.
matrixGenotype	A matrix of SNPs/INDELs coded: 0 for 0|0 or 0/0; 1 for 0/1, 1/0, 0|1, 1|0; 2 for 1/1, 1|1. Rows are SNPs/INDELs and columns are samples. If users use this argument then the argument vcfFile is not necessary.
cnvColumn	A number indicating the column of CNV.
popColumn	A number indicating the column of a population being calculated LD values.
population	A character() vector indicating names of populations.
chr	A character string indicating a chromosome of genes/SNPs/INDELs.
hg	A character string indicating the version of a reference genome (default: hg19).
st	A number indicating a starting coordinate to read the vcf file.
en	A number indicating an ending coordinate to read the vcf file.
nChunkForVcf	A number indicating how many chunks users would like to divide the vcf file to read into R. It depends on users' computers. We usually use 10 to 50 for this argument.
codeSNP	A character string indicating a way to code unphased/phased SNPs/INDELs into numeric values (Two: 0, 1 or Three: 0, 1, 2).
codeCNV	A character string partial matching to one of: “All” will test copy-number counts and SNPs/INDELs, “ThreeGroup” will divide samples into three groups: deletion, normality and duplication.
typeTest	A character string partial matching to one of: “All” will test all copy-number status, “Dup/Del” will test for only duplicated/deleted versus normal.
parallel	A logical value indicating whether multicores are used or NOT (default: FALSE).

Value

r2Andpvalues: A data frame (or a list) with each row for a SNP/INDEL: all information includes p-values adjusted by the method of Benjamini and Hocheberg (1995) and r2 values between the SNP/INDEL and copy-number status.

Note

st and en must not be outside the coordinates of the VCF file.

Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. [e-mail]

References

Benjamini, Y., and Hochberg, Y., 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57, 289-300.

See Also

fcgr3bMXL

Examples

##Load data: fcgr3bMXL in CNVrd2 package############
data(fcgr3bMXL)
##Name a vcf file (vcfFile)
vcfFile <- system.file(package="CNVrd2", "extdata",
                      "chr1.161600000.161611000.vcf.gz")
##Make a data fame named sampleCNV including samples, CNs, population names

sampleCNV <- data.frame(copynumberGroups$allGroups[, c(1,2) ],rep("MXL", 58))

rownames(sampleCNV) <- substr(sampleCNV[, 1], 1, 7)
sampleCNV[, 1] <- rownames(sampleCNV)
##The first column must be the sample names 
tagSNPandINDELofMXL <- calculateLDSNPandCNV(sampleCNV = sampleCNV,
                                 vcfFile = vcfFile, cnvColumn = 2,
                                 population = "MXL", popColumn = 3,
                                 nChunkForVcf = 5, chr = "1",
                                 st = 161600000, en = 161611000,
                                 codeSNP= "Three", codeCNV = "ThreeGroup")
tagSNPandINDELofMXL[1:3,]

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.