get_bins: Bin markers and select representative markers based on...

In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

Bin markers and select representative markers based on p-values.

Description

Create bins of an arbitrary size and select an arbitrary number of representative markers across bins with the smallest p-values.

Usage

get_bins(GI = NULL, GP = NULL, bin.size = 1e+07, nqtn = NULL,
  MaxBP = 1e+10)

Arguments

GI	A data frame with three columns: marker name, chromosome, and base-pair position.
GP	A data frame with four columns: marker name, chromosome, base-pair position, and p-value.
bin.size	An integer scalar. The size (in base-pairs) of each bin.
nqtn	An integer scalar. The number of pseudo-QTNs to select.
MaxBP	An integer scalar. A scaling factor used to generate unique marker IDs.

Details

Markers are binned into bins of arbitrary size and represented by the marker with the smallest p-value within each bin.

Value

A logical vector indicating whether or not a marker is a pseudo-QTN.

Author(s)

Zhiwu Zhang

amkusmec/FarmCPUpp documentation built on Dec. 16, 2024, 9:01 a.m.