EAF plot

EAF plot

eafPlot(
  x,
  reference,
  rs_x = "rs",
  rs_reference,
  freq_x = "freq",
  freq_reference,
  inverse_freq_x = T,
  inverse_freq_reference = F
)

Arguments

x

data.frame / list of data.frames (output of ds.GWAS) Single table of results or list of tables (default output of ds.GWAS).

reference

data.frame Reference table that at least contains: SNP rs IDs and minor (or major) allele frequency of reference.

rs_x

character (default "rs") Name of the column that contains the rs IDs on x

rs_reference

character Name of the column that contains the rs IDs on reference

freq_x

character (default "freq") Name of the column that contains the minor (or major) allele frequencies on x

freq_reference

character Name of the column that contains the minor (or major) allele frequencies on reference

inverse_freq_x

bool (default TRUE) Use TRUE if x contains major allele frequencies, use FALSE if x contains minor allele frequencies. The default is set to TRUE since the default output of ds.GWAS frequencies is major allele frequencies.

inverse_freq_reference

bool (default FALSE) Use TRUE if x contains major allele frequencies, use FALSE if x contains minor allele frequencies. The default is set to TRUE since usually reference panels report minor allele frequencies.

Value

A ggplot object

Details

Plotting the reported EAFs against a reference set, such as from the HapMap or 1000 Genomes projects, or from one specific study, can help visualize patterns that pinpoint strand issues, allele miscoding or the inclusion of individuals whose self-reported ancestry did not match their genetic ancestry.