correlateR: correlateR

In genesofeve/ProjectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

correlateR

Description

Function to extract genes highly correlated with a gene or reference expression pattern.

Usage

correlateR(genes, dat, threshtype = "R", threshold = 0.7, absR = FALSE, ...)

Arguments

genes	gene or character vector of genes for reference expression pattern
dat	matrix or data frame with genes to be used for to calculate correlation
threshtype	Default "R" indicates thresholding by R value or equivalent. Alternatively, "N" indicates a numerical cut off.
threshold	numeric indicating value at which to make threshold.
absR	logical indicating where to include both positive and negatively correlated genes
...	addtion inputs to cor, such as method

Details

If threshtype is "R" than threshold must be between -1 and 1. Otherwise if top N correlated genes are required, set threshtype as "N" and set threshold = N, i.e, the number of correlated genes required.

Value

A correlation matrix

Examples

cor2T<-correlateR(genes="T", dat=p.RNAseq6l3c3t, threshtype="N", threshold=10, absR=TRUE)

genesofeve/ProjectR documentation built on Nov. 16, 2024, 8:20 p.m.