prep: Infercnv-based preparation of relative gene expression...

In dkzhang777/SlideCNA: Calls Copy Number Alterations from Slide-Seq Data

Infercnv-based preparation of relative gene expression intensities

Description

This function takes in a data table of raw counts and a vector of reference/normal beads to normalize counts and adjust for reference expression.

Usage

prep(so, normal_beads, gene_pos, chrom_ord, logTPM = FALSE)

Arguments

so	Seurat object of Slide-seq data with raw counts
normal_beads	vector of names of normal beads
gene_pos	data.table with columns for GENE, chr, start, end, rel_gene_pos (1 : # of genes on chromosome)
chrom_ord	vector of the names of chromosomes in order
logTPM	TRUE if performing adjustment with logTPM

Value

A data.table of normalized, capped, and ref-adjusted counts with genomic psoition info

dkzhang777/SlideCNA documentation built on Jan. 25, 2025, 5:53 p.m.