make_plot_maf: MAF plot
In MRCIEU/mrQC: CheckSumStats

make_plot_maf

R Documentation

MAF plot

Description

Make a plot comparing minor allele frequency between test dataset and reference studies.

Usage

make_plot_maf(
  ref_dat = NULL,
  ref_1000G = c("AFR", "AMR", "EAS", "EUR", "SAS", "ALL"),
  target_dat = NULL,
  eaf = "eaf",
  snp_target = "rsid",
  snp_reference = "SNP",
  ref_dat_maf = "MAF",
  target_dat_effect_allele = "effect_allele",
  target_dat_other_allele = "other_allele",
  ref_dat_minor_allele = "minor_allele",
  ref_dat_major_allele = "major_allele",
  trait = "trait",
  target_dat_population = "population",
  ref_dat_population = "population",
  target_study = "study",
  ref_study = "study",
  Title = "Comparison of allele frequency between test dataset & reference study",
  Ylab = "Allele frequency in test dataset",
  Xlab = "MAF in reference study",
  cowplot_title = "Allele frequency in test dataset vs 1000 genomes super populations",
  return_dat = FALSE,
  nocolour = FALSE,
  legend = TRUE,
  allele_frequency_conflict = 1,
  publication_quality = FALSE
)

Arguments

`ref_dat`	user supplied reference dataset. data frame. optional
`ref_1000G`	if ref_dat is NULL, the user should indicate the 1000 genomes reference study of interest. options are: AFR, AMR, EAS, EUR, SAS or ALL. Default is to make plots for all super populations
`target_dat`	the test dataset of interest. Data frame.
`eaf`	name of the effect allele frequency column in target_dat
`snp_target`	rsid column in target_dat
`snp_reference`	rsid column in ref_dat
`ref_dat_maf`	name of the minor allele frequency column in the reference dataset. Only necessary if ref_dat is specified
`target_dat_effect_allele`	name of the effect allele column in target_dat
`target_dat_other_allele`	name of the non-effect allele column in target_dat
`ref_dat_minor_allele`	name of the minor allele column in the reference dataset. Only necessary if ref_dat is specified
`ref_dat_major_allele`	name of the major allele column in the reference dataset. Only necessary if ref_dat is specified
`trait`	name of the trait corresponding to target_dat
`target_dat_population`	population ancestry of target_dat
`ref_dat_population`	name of column describing population ancestry of reference dataset. Only necessary if ref_dat is specified
`target_study`	column in target_dat indicating name of target study
`ref_study`	column in reference study indicating name of reference study. Only necessary if ref_dat is specified
`Title`	plot title
`Ylab`	Y label
`Xlab`	X label
`cowplot_title`	title of overall plot
`return_dat`	if TRUE, the dataset used to generate the plot is returned to the user and no plot is made.
`nocolour`	if TRUE, allele frequency conflicts are illustrated using shapes rather than colours.
`legend`	include legend in plot. Default TRUE
`allele_frequency_conflict`	how to define allele frequency conflicts. 1= flag SNPs in the test dataset whose reported minor allele has frequency >0.5. 2= additionally flag SNPs with allele frequency differening by more than 10 points from allele frequency in the reference dataset. Default = 1
`publication_quality`	produce a very high resolution image e.g. for publication purposes. Default FALSE