addInfo: Adds new columns to the chromInfo and gene.index

In SingerLab/gac: Genetic Analysis of Cells

Adds new columns to the chromInfo and gene.index

Description

The function adds information at the bin and gene level by running addBinInfo, and addGeneInfo

Usage

addInfo(cnr, df, gdf = NULL, ...)

Arguments

cnr	a cnr bundle
df	a data.frame with the data to incorporate into chromInfo. Particularly useful for adding p-values, genetic effects, etc to the bins
gdf	a data.frame with the data to incorporate into gene.index. Particularly useful for adding p-values, genetic effects, etc to the genes
...	other parameters passed to addGeneInfo, subsequently to merge

Value

Returns a CNR object with added columns to the chromInfo and to the gene.index. e.g. p-values for genome wide scans,

Examples

data(cnr)

fakeBinPval <- data.frame(pval = runif(5000))

fakeGenePval <- data.frame(hgnc.symbol = cnr$gene.index$hgnc.symbol,
pval = runif(nrow(cnr$gene.index)))
                       
cnr <- addInfo(cnr, df = fakeBinPval, gdf = fakeGenePval)

head(cnr$chromInfo)
head(cnr$gene.index)

## add info only to bins

fakeBinPval2 <- data.frame(pval = runif(5000))
cnr <- addInfo(cnr, df = fakeBinPval2)

head(cnr$chromInfo)
head(cnr$gene.index)

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.