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library(vcfR)##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
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## [119] "last slide lecture 3.docx"
## [120] "Late Withdrawal Form.pdf"
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## [2] "all_loci-1.vcf"
## [3] "all_loci.vcf"
## [4] "ALL.chr22_GRCh38.genotypes.20170504.vcf"
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## [8] "vcfR_test.vcf"
## [9] "vcfR_test.vcf.gz"rd <- read.vcfR("22.1059792-1299792.ALL.chr22_GRCh38.genotypes.20170504.vcf",
convertNA = T)## Scanning file to determine attributes.
## File attributes:
## meta lines: 130
## header_line: 131
## variant count: 0
## column count: 2513
##
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 2513
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processedlibrary(vcfR)
getwd()
list.files()
list.files(pattern = "vcf")
rd <- read.vcfR("22.1059792-1299792.ALL.chr22_GRCh38.genotypes.20170504.vcf",
convertNA = T)You can also embed plots, for example:
Note that the echo = FALSE parameter was added to the
code chunk to prevent printing of the R code that generated the
plot.