makeAllPlots: Wrapper function to run all plotting and summary functions

In sarahcn/impplotr: Summarize Metrics from University of Michigan Imputation Server

Description

Wrapper function to run all plotting and summary functions

Usage

makeAllPlots(imp_dir, out_dir, start_chr = 1, end_chr = 23,
  sets = c("imputed", "masked"), plots = c("boxplot", "info_by_maf",
  "masked_check_strand"), fmt = "pdf", summary = TRUE, rsq_filt = 0.8,
  verbose = TRUE, maf_thresh = 0.05, parX = FALSE, keep_list = NA)

Arguments

imp_dir	Imputation directory
out_dir	Output directory
start_chr	Start chromosome (1:23)
end_chr	End chromosome (1:23)
sets	Sets of imputation summaries
plots	Sets of plots
fmt	Plot output format (only pdf supported)
summary	Logical indicator of whether to run impSummary
rsq_filt	Rsq threshold used in maskedPlots
verbose	Logical indicator for verbose reporting
maf_thresh	Minor allele frequency threshold for grouping masked variants in maskedSummary
parX	logical whether to include PAR (not implemented)
keep_list	File path of an initial variant keep list, with columns variant name and chromosome (integer)

sarahcn/impplotr documentation built on May 3, 2019, 9 p.m.