Run GoShifter enrichment pipeline

Run the GoShifter locus-specific enrichment pipeline. This function orchestrates the full workflow: preparing SNP maps and LD files, querying ROADMAP annotations, running the GoShifter permutation test, and collecting results.

Usage

GOSHIFTER(
  locus_dir,
  dat,
  SNP_group = "",
  goshifter_path = NULL,
  permutations = 1000,
  ROADMAP_search = "",
  chromatin_states = c("TssA"),
  R2_filter = 0.8,
  overlap_threshold = 1,
  force_new_goshifter = FALSE,
  remove_tmps = TRUE,
  verbose = TRUE,
  save_results = TRUE
)

Source

GoShifter GitHub Trynka et al. (2015) Am J Hum Genet

Arguments

locus_dir

Path to the locus-level results directory.

dat

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

SNP_group

Character string labelling this group of SNPs (default "").

goshifter_path

Path to the directory containing goshifter.py. If NULL, the bundled copy shipped with echolocatoR is used (see GOSHIFTER_find_folder).

permutations

Number of permutations for the enrichment test (default 1000).

ROADMAP_search

A keyword query passed to ROADMAP_query to filter ROADMAP annotations (e.g. "monocyte").

chromatin_states

Character vector of chromatin state abbreviations to test enrichment for (default c("TssA")).

R2_filter

LD r-squared threshold for GoShifter (default 0.8).

overlap_threshold

Minimum number of overlapping SNPs required before running GoShifter on an annotation (default 1).

force_new_goshifter

If TRUE, re-run even if results already exist on disk (default FALSE).

remove_tmps

Remove intermediate GoShifter output files after collecting results (default TRUE).

verbose

Print messages (default TRUE).

save_results

Write combined results to a tab-delimited file (default TRUE).

Value

A data.table of GoShifter enrichment results across all requested chromatin states.

See also

Other GOSHIFTER: GOSHIFTER_bed_names(), GOSHIFTER_check_overlap(), GOSHIFTER_create_LD(), GOSHIFTER_create_snpmap(), 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{
locus_dir <- echodata::locus_dir
dat <- echodata::BST1
gs_out <- GOSHIFTER(locus_dir = locus_dir, dat = dat)
} # }