prep {SlideCNA} | R Documentation |
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
[Package SlideCNA version 0.1.0 Index]