map.patchseq: Map PatchSeq

In NathanSkene/PatchseqMap: PatchseqMap

Description

Takes celltype specificity data ('ctd') and patchseq expression data ('patchdata') and returns which cell type each patchseq cell maps onto

Usage

map.patchseq(ctd, patchdata, sdThresh = 1, annotLevel = 2,
  useSDthresh = TRUE, reps = 10000)

Arguments

ctd	Cell type specificity data as generated by EWCE
patchdata	Gene by cell matrix of patchseq data
sdThresh	Genes from the patchseq data will only be kept if they have a standard devation across the dataset larger than this figure
annotLevel	Annotation level of ctd to use
useSDthresh	Should standard deviation or total reads be used to determine which patchseq genes to keep?
reps	How many bootstrap replicates to use. Ideally 10000.

Value

A list with assigned and fullRes

Examples

map.patchseq(ctd,patchdata_Reduced,sdThresh=1,annotLevel=2,useSDthresh=TRUE,reps=10000)

NathanSkene/PatchseqMap documentation built on May 17, 2019, 1:35 p.m.