Mercurial > repos > greg > coral_multilocus_genotype
comparison coral_multilocus_genotype.R @ 6:0488ca4a8c4e draft
Uploaded
author | greg |
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date | Wed, 11 Nov 2020 18:09:01 +0000 |
parents | 34e02e8b4232 |
children | bcb28b49b0cc |
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5:457cbc5ca604 | 6:0488ca4a8c4e |
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416 i <- ifelse(is.na(stag_db_report[3]), "", stag_db_report[[3]]); | 416 i <- ifelse(is.na(stag_db_report[3]), "", stag_db_report[[3]]); |
417 i <- i[!apply(i== "", 1, all), ]; | 417 i <- i[!apply(i== "", 1, all), ]; |
418 | 418 |
419 # Subset VCF to the user samples. | 419 # Subset VCF to the user samples. |
420 start_time <- time_start("Subsetting vcf to the user samples"); | 420 start_time <- time_start("Subsetting vcf to the user samples"); |
421 l <- length(i) + 1; | 421 affy_list <- append(stag_db_report$affy_id,"FORMAT"); |
422 svcf <- vcf[, 1:l]; | 422 svcf <- vcf[,colnames(vcf@gt) %in% affy_list]; |
423 write.vcf(svcf, "subset.vcf.gz"); | 423 write.vcf(svcf, "subset.vcf.gz"); |
424 vcf.fn <- "subset.vcf.gz"; | 424 vcf.fn <- "subset.vcf.gz"; |
425 snpgdsVCF2GDS(vcf.fn, "test3.gds", method="biallelic.only"); | 425 snpgdsVCF2GDS(vcf.fn, "test3.gds", method="biallelic.only"); |
426 genofile <- snpgdsOpen(filename="test3.gds", readonly=FALSE); | 426 genofile <- snpgdsOpen(filename="test3.gds", readonly=FALSE); |
427 gds_array <- read.gdsn(index.gdsn(genofile, "sample.id")); | 427 gds_array <- read.gdsn(index.gdsn(genofile, "sample.id")); |