readVariantsFromFile: Read variants from disk
In tkonopka/RGeneticThesaurus: Analysis of thesaurus-annotated genomic variants
Description
Read variants from disk and perform some pre-processing. In contrast to
obtaining a data.frame using read.table(), this function does not crash
when a vcf file does not have any valid rows (i.e. no variants detected).
This function also automatically allows the user to discard some columns
of the input table.
Usage
1
2
readVariantsFromFile(ff, n = 4096, ignorelines = c("thesaurushard",
"thesaurusmany"), getcolumns = 10, withindels = FALSE)
Arguments
ff
filename
n
integer, determines how many lines are read from the input to scan for the
vcf header. Set this to a moderatly large number, i.e. larger than the expected number
of header lines in the vcf file.
ignorelines
vector of filter codes. Lines in the vcf that contain one
of these filter codes will be eliminated, i.e. not reported in the output
getcolumns
number of columns to read/return. Use this to select only a few of the columns of
the vcf table (ignoring the info or format fields can save memory)
withindels
logical. Set to TRUE to return all variants in input vcf, or
set to FALSE to obtain only single-nucleotide substitutions,
tkonopka/RGeneticThesaurus documentation built on May 31, 2019, 3:44 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
Read variants from disk and perform some pre-processing. In contrast to obtaining a data.frame using read.table(), this function does not crash when a vcf file does not have any valid rows (i.e. no variants detected). This function also automatically allows the user to discard some columns of the input table.
Usage
1 2 | readVariantsFromFile(ff, n = 4096, ignorelines = c("thesaurushard",
"thesaurusmany"), getcolumns = 10, withindels = FALSE)
|
Arguments
ff |
filename |
n |
integer, determines how many lines are read from the input to scan for the vcf header. Set this to a moderatly large number, i.e. larger than the expected number of header lines in the vcf file. |
ignorelines |
vector of filter codes. Lines in the vcf that contain one of these filter codes will be eliminated, i.e. not reported in the output |
getcolumns |
number of columns to read/return. Use this to select only a few of the columns of the vcf table (ignoring the info or format fields can save memory) |
withindels |
logical. Set to TRUE to return all variants in input vcf, or set to FALSE to obtain only single-nucleotide substitutions, |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.