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Read PLINK allele-frequency files (.frq) into one table

Source: R/sldscWrapper.R
readSldscFrq.Rd

Reads the per-chromosome PLINK `.frq` files for the reference panel and stacks them into a single data.frame of CHR, SNP, MAF. Feeds the frq slot of SldscData.

Usage

readSldscFrq(frqfileDir, plinkName = "ADSP_chr")

Arguments

frqfileDir

Character. Directory of `.frq` files.

plinkName

Character. Filename prefix (files at `<plinkName><chr>.frq`). Falls back to all `*.frq` in the directory when the prefix matches nothing.

Value

A data.frame: CHR, SNP, MAF.

Examples

sldsc <- system.file("extdata", "sldsc", package = "pecotmr")
readSldscFrq(sldsc, plinkName = "reference.")
#> New names:
#> • `` -> `...1`
#> • `` -> `...3`
#> • `` -> `...4`
#> • `` -> `...5`
#> • `` -> `...6`
#> • `` -> `...7`
#> • `` -> `...8`
#> • `` -> `...9`
#> • `` -> `...10`
#> • `` -> `...11`
#> • `` -> `...13`
#> • `` -> `...14`
#> • `` -> `...16`
#> • `` -> `...17`
#> • `` -> `...19`
#> • `` -> `...20`
#> • `` -> `...21`
#> • `` -> `...22`
#> • `` -> `...23`
#> • `` -> `...24`
#> • `` -> `...25`
#> • `` -> `...26`
#> • `` -> `...27`
#> • `` -> `...29`
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#>   dat <- vroom(...)
#>   problems(dat)
#> # A tibble: 343 × 3
#>    CHR   SNP     MAF
#>    <lgl> <chr> <dbl>
#>  1 NA    NA      978
#>  2 NA    NA      978
#>  3 NA    NA       NA
#>  4 NA    NA       NA
#>  5 NA    A       978
#>  6 NA    C        NA
#>  7 NA    NA      978
#>  8 NA    NA       NA
#>  9 NA    T        NA
#> 10 NA    C        NA
#> # ℹ 333 more rows