comparison coral_multilocus_genotype.R @ 6:0488ca4a8c4e draft

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5:457cbc5ca604

i <- ifelse(is.na(stag_db_report[3]), "", stag_db_report[[3]]);
i <- i[!apply(i== "", 1, all), ];

# Subset VCF to the user samples.
start_time <- time_start("Subsetting vcf to the user samples");
l <- length(i) + 1;
svcf <- vcf[, 1:l];
write.vcf(svcf, "subset.vcf.gz");
vcf.fn <- "subset.vcf.gz";
snpgdsVCF2GDS(vcf.fn, "test3.gds", method="biallelic.only");
genofile <- snpgdsOpen(filename="test3.gds", readonly=FALSE);
gds_array <- read.gdsn(index.gdsn(genofile, "sample.id"));

6:0488ca4a8c4e

i <- ifelse(is.na(stag_db_report[3]), "", stag_db_report[[3]]);
i <- i[!apply(i== "", 1, all), ];

# Subset VCF to the user samples.
start_time <- time_start("Subsetting vcf to the user samples");
affy_list <- append(stag_db_report$affy_id,"FORMAT");
svcf <- vcf[,colnames(vcf@gt) %in% affy_list];
write.vcf(svcf, "subset.vcf.gz");
vcf.fn <- "subset.vcf.gz";
snpgdsVCF2GDS(vcf.fn, "test3.gds", method="biallelic.only");
genofile <- snpgdsOpen(filename="test3.gds", readonly=FALSE);
gds_array <- read.gdsn(index.gdsn(genofile, "sample.id"));