Description Usage Arguments Value
Create a Manhattan plot using ggplot2 on either RDS or FBM object GWAS results.
1 | pvdiv_manhattan(effects, ind = NULL, snp = NULL, thr = NULL, ncores = 1)
|
effects |
Either a gwas effects RDS or FBM object created using 'pvdiv_standard_gwas' (with savetype = "rds" or savetype = "fbm"). If a fbm, this file is saved under the name "gwas_effects_suffix.rds" and can be loaded into R using the bigstatsr function "big_attach". |
ind |
If effects is a FBM object, this should be the row number of the phenotype from the associated metadata for the FBM object. |
snp |
If effects is a FBM object, you must also supply a "bigSNP" object;
load into R with |
thr |
Numeric. Significance threshold plotted as a horizontal line. Default is Bonferroni. |
ncores |
Integer. Number of cores to use for parallelization. |
A ggplot2 plot.
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