Create GoShifter SNP-map file

Prepare the tab-delimited SNP-map input file required by GoShifter. The file contains columns SNP, Chrom (prefixed with "chr"), and BP.

GOSHIFTER_create_snpmap(dat, GS_results, verbose = TRUE)

Arguments

dat

A data.table or data.frame with columns SNP, CHR, and POS.

GS_results

Path to the GoShifter results directory where the snpmap.txt file will be written.

verbose

Print messages (default TRUE).

Value

Path to the written snpmap.txt file (invisibly).

See also

Other GOSHIFTER: GOSHIFTER(), GOSHIFTER_bed_names(), GOSHIFTER_check_overlap(), GOSHIFTER_create_LD(), GOSHIFTER_find_folder(), GOSHIFTER_get_roadmap_annotations(), GOSHIFTER_heatmap(), GOSHIFTER_histograms_SNPgroups(), GOSHIFTER_histograms_pvals(), GOSHIFTER_list_chromatin_states(), GOSHIFTER_process_results(), GOSHIFTER_run(), GOSHIFTER_search_ROADMAP(), GOSHIFTER_summarise_results()

Examples

if (FALSE) { # \dontrun{
dat <- echodata::BST1
locus_dir <- echodata::locus_dir
snpmap <- GOSHIFTER_create_snpmap(
    dat = dat,
    GS_results = file.path(locus_dir, "GoShifter")
)
} # }