Software Checkpoint: Loading your VCF file into R

List.files()

getwd()

## [1] "/Users/angelazhu/Desktop/Biosc1540"

list.files(pattern = "vcf")

## [1] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504.vcf.gz"
## [2] "14.36255114-36495114.ALL.chr14_GRCh38.genotypes.20170504.vcf.gz"
## [3] "code_checkpoint_vcfR.html"                                      
## [4] "code_checkpoint_vcfR.Rmd"

my_vcf <- "14.36255114-36495114.ALL.chr14_GRCh38.genotypes.20170504.vcf.gz"

vcf <- vcfR::read.vcfR(my_vcf, 
                       convertNA = T)

## Scanning file to determine attributes.
## File attributes:
##   meta lines: 130
##   header_line: 131
##   variant count: 6190
##   column count: 2513
## 
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 6190
##   Character matrix gt cols: 2513
##   skip: 0
##   nrows: 6190
##   row_num: 0
## 
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant 6000
Processed variant: 6190
## All variants processed