CellTagWhitelistFiltering: CellTag Whitelist Filtering Function

In morris-lab/CloneHunter: Identify Clonal Identity from ScRNA-Seq and CellTag Data

Description

This function conducts whitelist filtering such that only CellTags with count number over their certain percentile would be considered for clone calling

Usage

CellTagWhitelistFiltering(count.sorted.table, percentile, output.dir,
  output.count.file, save.output = TRUE)

Arguments

count.sorted.table	The count table for all CellTags with first column being CellTag and second being counts.
percentile	A fraction cutoff percentile for filtering the CellTags e.g. 0.9 for 90th percentile
output.dir	Which directory would you like to store these files?
output.count.file	Which CSV filename would you like to save to for the filtered count table? Default to NULL. If NULL but save.output = TRUE, automatic names will be generated and used for storage
save.output	Would you like to save your whitelisted counts to file? Default to TRUE

Value

Whitelisted CellTag count table

Examples

CellTagWhitelistFiltering("data.txt", 0.9, "~/Desktop/", "My_Favourite_Whitelist.csv")

morris-lab/CloneHunter documentation built on June 12, 2019, 11:01 a.m.