Read target annotation files (.annot.gz) into one table

Reads the per-chromosome polyfun `.annot.gz` files in a directory and stacks them into a single data.frame of CHR, SNP, and the annotation columns. This is the I/O step feeding the annot slot of SldscData; the computation (computeSldscAnnotSd, isBinarySldscAnnot) then runs on the loaded table, not on paths.

Usage

readSldscAnnot(targetAnnoDir, annotCols = NULL)

Arguments

targetAnnoDir: Character. Directory of `.annot.gz` files.
annotCols: Character or integer vector, default NULL. Annotation columns to keep. NULL keeps all non-standard columns (auto-detected).

Value

A data.frame: CHR, SNP, and annotation columns.

Examples

sldsc <- system.file("extdata", "sldsc", package = "pecotmr")
readSldscAnnot(sldsc)
#> # A tibble: 15,707 × 3
#>      CHR SNP         ANNOT
#>    <dbl> <chr>       <dbl>
#>  1     2 rs10171242      0
#>  2     2 rs142050900     0
#>  3     2 rs193013484     0
#>  4     2 rs6749571       0
#>  5     2 rs6761187       0
#>  6     2 rs447775        0
#>  7     2 rs115023044     0
#>  8     2 rs78475392      0
#>  9     2 rs6740037       0
#> 10     2 rs12714398      0
#> # ℹ 15,697 more rows