Import SNP based statistics

Source: R/hypogen_import.R

hypo_import_snps imports SNP based statistics (such as VCFtools output).

hypo_import_snps(file, gz = FALSE, run, ...)

Arguments

file

string scalar (mandatory), the input file
gz

logical scalar (optional), is the input file gz compressed?
run

string scalar (optional), appends a column RUN as ID if several files should be merged later
...

parameters passed to vroom::vroom()

Details

This function imports SNP based statistics. The input is expected to be tab separated, to contain a CHROM and POS column and can optionally be gz compressed. After import, the CHROM based position is transposed to a genome wide position for continuous visualization.

See also

hypo_import_windows

Examples


file_snps <- system.file("extdata", "example.weir.fst.gz", package = "hypogen")

hypo_import_snps(file = file_snps, gz = TRUE)

#> Rows: 235
#> Columns: 3
#> Delimiter: "\t"
#> chr [1]: CHROM
#> dbl [2]: POS, WEIR_AND_COCKERHAM_FST
#> 
#> Use `spec()` to retrieve the guessed column specification
#> Pass a specification to the `col_types` argument to quiet this message
#> # A tibble: 235 x 5
#>    CHROM   POS WEIR_AND_COCKERHAM_FST GSTART  GPOS
#>    <chr> <dbl>                  <dbl>  <dbl> <dbl>
#>  1 LG01    321             -0.0134         0   321
#>  2 LG01   1258             -0.0112         0  1258
#>  3 LG01   1373              0.00286        0  1373
#>  4 LG01   1398              0.00686        0  1398
#>  5 LG01   1403             -0.0000585      0  1403
#>  6 LG01   1494             -0.00282        0  1494
#>  7 LG01   1495             -0.0114         0  1495
#>  8 LG01   2121              0.0148         0  2121
#>  9 LG01   3079              0.0145         0  3079
#> 10 LG01   3085             -0.0136         0  3085
#> # … with 225 more rows