VCF_read_snp_diplo_bial_int_altpresence: (OBSOLETE) Read batch of biallelic SNP data into matrices

In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description

OBSOLETE : please refer to documentation for "VCF_snpmat_diplo_bial_geno_filtered" to find out about their replacements.

Reads biallelic SNP data in different representations into pre-allocated matrices.

Usage

VCF_read_snp_diplo_bial_int_altpresence( vcffh , mat )
VCF_read_snp_diplo_bial_int_nuclcodes( vcffh , mat )
VCF_read_snp_diplo_bial_str_01( vcffh , mat )
VCF_read_snp_diplo_bial_str_allelechars( vcffh , mat )
VCF_read_snp_diplo_bial_str_nuclcodes( vcffh , mat )

Arguments

vcffh	VCF file handle as returned by vcf_open
mat	A matrix of either integer or string type, corresponding to _str_ or _int_ named methods

Details

OBSOLETE : please refer to documentation for "VCF_snpmat_diplo_bial_geno_filtered" to find out about their replacements.

Prerequisites are: - a valid, open VCF file handle, passed as vcffh - a valid sample selection (vcf_getsamples,vcf_getselectedsamples,vcf_selectsmaples) - a properly set region (vcf_setregion) - and a result matrix, mat.

The matrix will be filled with allele data in one of 4 encodings and needs to be of either integer or character data type, both depending on the called function (VCF_..._int_... or VCF_..._str_...) . Each column corresponds to a SNP locus and each row to a sample. The number of matrix columns determines the maximum number of SNP loci that are parsed from the VCF. Column names are set to the position of the SNP, the row names are named after the samples they represent. There must be at least as many rows as selected samples. Unused rows will be filled with default (N) data. If there are not enough SNPs to fill all columns, the unused columns will be numbered with -1 and filled with N or -1.

VCF data is required to be diploid.

Representations:

• int_altpresence : 0 if genotype is REF/REF, 1 if not

• int_nuclcodes : integers, two-digit numbers: 11=TT, 12=TC, 13=TG, 14=TA, 15=TN, 21=CT, etc. (1=T, 2=C, 3=G, 4=A, 5=N)

• str_01 : string, either 00, 01, 10 or 11 : 00=ref/ref, 11=alt/alt, 10=alt/ref, 01=ref/alt

• str_allelechars : string, nucleotides of both chromosomes (no indication of reference allele)

• str_nuclcodes : string, two-digit numbers: 11=TT, 12=TC, 13=TG, 14=TA, 15=TN, 21=CT, etc. (1=T, 2=C, 3=G, 4=A, 5=N)

Value

TRUE or FALSE

Author(s)

Ulrich Wittelsbuerger

See Also

VCF_snpmat_diplo_bial_geno_filtered

Examples

	warning("These functions are obsolete! Consult VCF_snpmat_diplo_bial_geno_filtered etc.")

WhopGenome documentation built on May 1, 2019, 10:12 p.m.