correctIndices: Calculate the correct indices for the output of...

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Calculate the correct indices for the output of correlationTest

Description

Consider the upper triangular portion of a matrix of size nxn. Results from the correlationTest are output as the combination of two vectors, correlation statistic and p-values. The order of the output is 1vs2, 1vs3, 1vs4, etc. The correctIndices returns the correct indices to fill a correlation matrix or correlation-pvalue matrix.

Usage

correctIndices(n)

Arguments

n	The number of features compared by correlationTest (nrow(mat)).

Value

A vector of the indices for an upper triangular matrix.

See Also

correlationTest

Examples

data(mouseData)
mat = MRcounts(mouseData)[55:60,]
cors = correlationTest(mat)
ind  = correctIndices(nrow(mat))

cormat = as.matrix(dist(mat))
cormat[cormat>0] = 0
cormat[upper.tri(cormat)][ind] = cors[,1]
table(cormat[1,-1] - cors[1:5,1])

HCBravoLab/metagenomeSeq documentation built on March 17, 2024, 3:21 p.m.