correlateR: correlateR

Description Usage Arguments Details Value Examples

View source: R/correlateR.R

Description

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

Usage

1
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

1
cor2T<-correlateR(genes="T", dat=p.RNAseq6l3c3t, threshtype="N", threshold=10, absR=TRUE)

projectR documentation built on Nov. 8, 2020, 7:50 p.m.