plot_gemma_lmm: Plot the GWAS results as a Manhattan plot and highlight...

In TheJacksonLaboratory/mousegwas: Run in-bred mouse GWAS

Description

Plot the GWAS results as a Manhattan plot and highlight specific genes

Usage

plot_gemma_lmm(
  results_file,
  name = "GWAS results",
  metasoft = FALSE,
  pyLMM = FALSE,
  annotations = NULL,
  namethr = 5,
  redthr = 4,
  diff = NULL,
  genotypes = NULL,
  maxdist = 1e+06,
  corrthr = 0.6,
  test = "p_wald",
  addgenes = TRUE,
  annot = NULL
)

Arguments

results_file	A GEMMA results file
name	The title
metasoft	set TRUE if the input is metaSOFT output
pyLMM	TRUE if the input is pyLMM output with rs ID in the first column SNP_ID
annotations	If metasoft is TRUE then annoattions file should be given
namethr	Print gene name above this threshold
redthr	Red points above this thr
diff	A file with results to be subtracted from the first file. Must be in the same format, only implemented for GEMMA
genotypes	The genotypes of the input strains to compute correlation. If given (as data.frame with row.names) every peak will be colored
maxdist	maximal distance between peak and related SNPs
corrthr	r-square threshold to consider SNPs in the same peak, combined with maxdist
test	Name of test to use
addgenes	A boolean. Add gene names or not
annot	Genes table, optional. If NULL pull from biomaRt

Value

An object with the plot object, (plot), The GWAS results (gwas) and the plotted object (pwas)

TheJacksonLaboratory/mousegwas documentation built on Sept. 27, 2021, 9:14 a.m.