Adjustment of marker summary statistics using clumping and thresholding
Source:R/genomic_statistics.R
adjStat.RdAdjust marker summary statistics using linkage disequilibrium information from Glist.
Usage
adjStat(
stat = NULL,
Glist = NULL,
chr = NULL,
statistics = "b",
r2 = 0.9,
ldSets = NULL,
threshold = 1,
header = NULL,
method = "pruning"
)Arguments
- stat
A data frame with marker summary statistics (see required format above).
- Glist
List of information about genotype matrix stored on disk.
- chr
Chromosome(s) being processed.
- statistics
Specify what type of statistics ("b" or "z") is being processed. Default is "b".
- r2
Threshold used in clumping/pruning procedure. Default is 0.9.
- ldSets
List of marker sets - names correspond to row names in `stat`.
- threshold
P-value threshold used in clumping procedure. Default is 1.
- header
Character vector with column names to be excluded in the LD adjustment.
- method
Method used in adjustment for linkage disequilibrium. Default is "clumping".
Details
Required input format for summary statistics:
stat can be a data.frame(rsids, chr, pos, ea, nea, eaf, b, seb, stat, p, n) (single trait)
stat can be a list(marker=(rsids, chr, pos, ea, nea, eaf), b, seb, stat, p, n) (multiple trait)
For details about the summary statistics format, see the main function description.