checkchunksize: Check chunk size

In episcan: Scan Pairwise Epistasis

Description

Check the chunk size whether it is over the given number of variables(vaiants) in genotype data. If yes, reset the chunk size equal to the number of variables(vaiants).

Usage

checkchunksize(c, m, n = NULL, ...)

Arguments

c	an integer indicating the set chunk size.
m	an integer indicating the number of variables(vaiants) in geno1 if there is only one genotype input.
n	an integer indicating the number of variables(vaiants) in geno2 if there are two genotype inputs. The default is NULL.
...	not used.

Value

an integer indicating the chunk size

Examples

set.seed(123)
geno1 <- matrix(sample(0:2, size = 1000, replace = TRUE, prob = c(0.5, 0.3, 0.2)), 
ncol = 10)
geno2 <- matrix(sample(0:2, size = 2000, replace = TRUE, prob = c(0.4, 0.3, 0.3)), 
ncol = 20)

# if chunk size is smaller, there is no problem
chunksize <- 10
checkchunksize(chunksize, ncol(geno1))

# if chunk size is bigger than the number of columns in genotype input, 
# set chunk size equal to the number of columns in genotype input
chuksize <- 12
checkchunksize(chunksize, ncol(geno1))

# if chunk size is bigger than the number of columns of geno1 and geno2, 
# set chunk size equal to the minima nunumber of columns of geno1 and geno2
chunksize <- 50
checkchunksize(chunksize, ncol(geno1), ncol(geno2))

episcan documentation built on May 2, 2019, 9:42 a.m.