Package 'LinTInd'

align_to_range

Description

Title

Usage

align_to_range(p, s, cut)

Arguments

p	A base sequence in character format
s	A base sequence in character format
cut	The distance between the starting sites of two fragments

Value

A list include two IRanges instances (deletion and insertion)

Examples

align_to_range(p="AAGG---AAATTTCGGAATAAGGAATTT",s="AAGGCCCCAAATTT-CGGAATAAGGAATTT",cut=0)

---

BuildTree

Description

Generate an array generant tree of a data.tree data structure and save it

Usage

BuildTree(tag)

Arguments

tag	List generate from TagProcess, for more see TagProcess

Details

Title

Value

list with two elements, a data.tree data structure and a dataframe of array information for each cell barcode

Examples

data("example_data",package = "LinTInd")
treeinfo<-BuildTree(tag)

---

example of cellsinfo

Description

This an example of cellsinfo

Usage

data("example_data")

Format

cellsinfo

---

example of celltype

Description

This an example of celltype

Usage

data("example_data")

Format

celltype

---

change_form_stat

Description

Title

Usage

change_form_stat(indel)

Arguments

indel

List include two IRanges instances, contain start and end site of deletions and inserstions

Value

A scar form string

Examples

data("example_data",package = "LinTInd")
change_form_stat(cellsinfo$indel[[1]])

---

example of cutsite

Description

This an example of cutsite

Usage

data("example_data")

Format

cutsite

---

example of data

Description

This an example of data

Usage

data("example_data")

Format

data

---

example_data

Description

A set of example data

Usage

data("example_data")

Format

The format is: chr "example_data"

Examples

data("example_data",package = "LinTInd")

---

FindIndel

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)

---

IndelForm

Description

Generate scar form strings from scarinfo list for each reads

Usage

IndelForm(scarinfo, cln)

Arguments

scarinfo	List generate from FindIndel, for more see FindIndel
cln	The number of threads

Details

Title

Value

A new list of scarinfo, the scarform of each reads will add in the data frame of reads' informations

Examples

data("example_data",package = "LinTInd")
IndelForm(scarinfo,cln=1)

---

IndelIdents

Description

Function to define a scarform for each cell(single cell) or each reads(bulk seq, generate 'cell barcode' for each reads)

Usage

IndelIdents(scarinfo, method.use = NULL, cln)

Arguments

scarinfo	List generate from IndelForm, for more see IndelForm
method.use	Select how to determine a scar form string for each cell: "reads.num" (default):find the scar with the most reads in the cell; "umi.num":find the scar with the most UMIs in the cell; "consensus":find the consistent sequences in each cell, and then generate scar form strings from the new reads
cln	The number of threads

Details

Title

Value

The list generate from FindIndel, but in 'Scar' element a new column contain scar form strings

Examples

data("example_data",package = "LinTInd")
IndelIdents(scarinfo,method.use="umi.num",cln=1)

---

IndelPlot

Description

Return 2 line charts, show the probability of insertion and deletion at each site

Usage

IndelPlot(cellsinfo)

Arguments

cellsinfo

List generate from IndelIdents, for more see IndelIdents

Details

Title

Value

2 line charts

Examples

data("example_data",package = "LinTInd")
IndelPlot(cellsinfo = cellsinfo)

---

PlotTree

Description

Function to visualise the array generate tree

Usage

PlotTree(treeinfo, data.extract = NULL, annotation = NULL, prefix = NULL)

Arguments

treeinfo	List generate from BuildTree, for more see BuildTree
data.extract	(optional) If "FALSE" (default), will not return the indel's information, if it's "TRUE", the opposite
annotation	(optional) If "TRUE" (default), the annotation of each cell barcodes have to be provided before, and a heatmap of cells' distribution for each array will be return
prefix	(optional) Indels' prefix

Details

Title

Value

A list include a ggplot object, a dataframe show the distribution of each array contained in each group of cells (optional), and a dataframe to create the ggplot object

Examples

data("example_data",package = "LinTInd")
plotinfo<-PlotTree(treeinfo = treeinfo,data.extract = "TRUE",annotation = "TRUE")
plotinfo<-PlotTree(treeinfo = treeinfo,data.extract = "TRUE",annotation = "FALSE")

---

ReadCutsite

Description

Function to create a reference dataframe include each position and its' group

Usage

ReadCutsite(segref,reftype=NULL)

Arguments

segref	The cutsite file
reftype	Choose the reference type you want, if reftype="Accurate" (default), there will only the target sites be generated; if reftype="All", each site will be generated

Details

Title

Value

reference dataframe

Examples

data("example_data",package = "LinTInd")
ReadCutsite(cutsite)
ReadCutsite(cutsite,reftype="All")

---

ReadFasta

Description

Function to read fasta file to DNAString object

Usage

ReadFasta(filename)

Arguments

filename

The input fasta file name

Details

Title

Value

A DNAString object

Examples

fafile=paste0(system.file("extdata",package = 'LinTInd'),"/V3.fasta")
ReadFasta(fafile)

---

example of ref

Description

This an example of ref

Usage

data("example_data")

Format

ref

---

example of scarform

Description

This an example of scarform

Usage

data("example_data")

Format

scarform

---

example of scarinfo

Description

This an example of scarinfo

Usage

data("example_data")

Format

scarinfo

---

example of scarref

Description

This an example of scarref

Usage

data("example_data")

Format

scarref

---

example of scarref_all

Description

This an example of scarref_all

Usage

data("example_data")

Format

scarref_all

---

example of tag

Description

This an example of tag

Usage

data("example_data")

Format

tag

---

TagDist

Description

If the cell barcode and the anntation of each cell are provided, this function can calculate the relationship between each cell type in three way

Usage

TagDist(tag, method = NULL)

Arguments

tag	List generate from TagProcess, for more see TagProcess
method	Denote which method to use: "Jaccard"(default): calculate the weighted jaccard similarity of indels between each pair of groups; "P": right-tailed test, compare the Indels intersection level with the hypothetical result generated from random editing, and the former is expected to be significantly higher than the latter; "spearman": Spearman correlation of indels between each pair of groups

Details

Title

Value

2 figures are saved to show the distribution of INDEL and the relationship between groups respectively, the matrix of the relationship between groups is returned

Examples

tag_dist=TagDist(tag,method = "spearman")
tag_dist=TagDist(tag)
tag_dist=TagDist(tag,method = "Jaccard")
tag_dist=TagDist(tag,method = "P")
tag_dist=TagDist(tag,method = "spearman")

---

TagProcess

Description

Split each indel from scar form strings and map indel information to cell barcodes

Usage

TagProcess(data, Cells = NULL, prefix = NULL)

Arguments

data	List generate from IndelIdents, for more see IndelIdents
Cells	(optional) Dataframe of cells' annotation, with two columns: "Cell.BC" and "Cell.type"
prefix	(optional) Indels' prefix

Details

Title

Value

List with two dataframes: Indels for each cell barcode and cells' annotation

Examples

data("example_data",package = "LinTInd")
TagProcess(cellsinfo$info,Cells=celltype)

---

example of treeinfo

Description

This an example of treeinfo

Usage

data("example_data")

Format

treeinfo

---