FindIndel: FindIndel

In mana-W/LinTInd: Lineage tracing by indels

Description

This function can ident indels for each reads in input data, and create IRanges instances for deletion and insertion

Usage

FindIndel(
  data,
  scarfull,
  scar,
  align_score = NULL,
  type = NULL,
  indel.coverage = NULL,
  cln
)

Arguments

data	data frame, include cell barcode, UMI and reads.
scarfull	DNAString of reference sequence
scar	The cutsite data frame
align_score	The minimum alignment score that matched sequence should get, default in this parameter is the score that the reads which all of the target set were cutted got
type	Group name for this data ("None" in default)
indel.coverage	Choose indels selected scope: "Accurate" (default) means only the indles happenned in target site will be idented; "All" means each indel will be detected even they locate on the anchors
cln	The number of threads

Details

Title

Value

list include IRanges instances (deletion and insertion), a data frame of reads' informations, reference sequenc, dataframe of cut sites

Examples

data("example_data",package = "LinTInd")
scarinfo<-FindIndel(data=data,scarfull=ref,scar=cutsite,indel.coverage="All",type="test",cln=1)

mana-W/LinTInd documentation built on Feb. 14, 2022, 10:13 a.m.