IterRandPick: A function to iterate significant snps counting in a genotype...

In laurentlab-mpipz/rsurvival: Process genotype data from survival experiment

Description

A function to iterate significant snps counting in a genotype matrx with a random permutation of the survival vector

Usage

IterRandPick(gt, survival, max.p.neutral = 0.01, iter = 10,
  odded.pos = NULL, verbose = TRUE)

Arguments

gt	A genotype matrix
survival	A survival vector to shuffle
max.p.neutral	A threshold for p.neutral under which the snp will be counted (default is 0.01)
iter	Number of iteration (default is 10)
odded.pos	Optional. Reference to a variant in gt as a string. Iterate random pick according to the observed odds of genotype at this position in the genome.
verbose	Logical. If TRUE (default), report status of the process along the execution.

Value

An integer vector. Each item is the number of snps with low p.neutral value in gt data frame after a random permutation of the survival vector. Countains iter items.

See Also

For more detail, see PermutRandSurv and CountSignSnps which this function bind.

Examples

## Not run: 
IterRandomPick(gt, survival)
IterRandomPick(gt, survival, max.p.neutral = 0.05)
IterRandomPick(gt, survival, iter = 1000, verbose = FALSE)

## End(Not run)

laurentlab-mpipz/rsurvival documentation built on May 29, 2019, 9:14 a.m.