all_but_one_coco: all_but_one_coco

In theboocock/coco: Correlation-based conditional analysis

Description

All but one coco conditional analysis wrappper.

Usage

all_but_one_coco(data_set, ld_matrix, stepwise_p = 0.001, var_y = 1.6421,
  joint_step = T, joint_all = T, reported_p = 0.001)

Arguments

data_set	data.frame. Coco formatted input data.
ld_matrix	matrix. LD matrix ordered by postiion
stepwise_p	float. P-value threshold for forward-stepwise step.
var_y	float. Phenotypic variance for Y, if not specified it will be estimated using estimate_vary.
joint_step	boolean (T) = perform joint estimation when doing stepwise selection. (F) = perform conditional estimation when doing stepwise selection.
joint_all	boolean (T) = perform joint estimation when performing all but one analysis (F) = perform conditional estimation when performing all but one analysis.
hwe_variance	boolean. Force the use of Hardy-weinberg equillibrium when calculating the genotypic variance.
exact	boolean. Perform an exact analysis, extra data checks used in prep_data_set_common

Details

all_but_one_coco Performs a full all_but_one conditional analysis from the raw data.

Author(s)

James Boocock and Eli Stahl

theboocock/coco documentation built on May 31, 2019, 9:10 a.m.