test.single: Conduct single test

In rauschenberger/spliceQTL: Alternative Splicing

Description

This function tests for alternative splicing.

Usage

test.single(Y, X, map, i, limit = NULL, steps = NULL, W = NULL,
  w.type = NULL)

Arguments

Y	exon expression: matrix with n rows (samples) and p columns (exons)
X	SNP genotype: matrix with n rows (samples) and q columns (SNPs)
map	list with names "genes", "exons", and "snps" (output from map.genes, map.exons, and map.snps)
i	gene index: integer between 1 and nrow(map$genes)
limit	cutoff for rounding p-values
steps	size of permutation chunks: integer vector
W	numeric matrix: a square matrix with as many rows as there are covariates in the independent data set It represents the correlation structure expected in the independent data
w.type	string: if W=NULL and w.type is a given string, take the type: "cov" is the only one allowed. Then the inner product of the indep data X is taken

Details

The maximum number of permutations equals sum(steps). Permutations is interrupted if at least limit test statistics for the permuted data are larger than the test statistic for the observed data.

Examples

NA

rauschenberger/spliceQTL documentation built on May 13, 2019, 3:02 a.m.