correlateR {projectR} | R Documentation

## 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)

[Package projectR version 1.0.0 Index]