CNV_alterations: CNV in p and q arms of chromosome

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

CNV in p and q arms of chromosome

Description

Use single cell RNA-Seq expression data to identify copy number variation at chromosomal level such as deletions or gains of entire chromosome or large segments of chromosome

Usage

CNV_alterations(
  data_list = list(),
  data_id = list(),
  min_Sample = 5,
  min_Gene = 1500,
  path = " ",
  GenePositionFile = " ",
  threads_no = 8,
  MetaData = list(),
  Groupby = " ",
  cutoff = 1,
  Reference_name = " ",
  obs.title = "Observations",
  ref.title = "References",
  out.Filename = "inferCNV",
  cluster_by_groups = "FALSE"
)

Arguments

data_list	List of raw expression matrix. Genes should be in rows and cells should be in columns in each data in the list.
data_id	List of names/ids of expression matrix
min_Sample	gene filter, filter out genes which are not expressed in at least min_Sample cells
min_Gene	cell filter, filter out those cells which do not express at least min_Gene genes
path	Path of output directory to save results
GenePositionFile	A gene/chromosome positions file with chromosome name, start, end position. "genecode hg19" positional file is given with this package. Either you can use same using unCTC::gencode_v19_gene_pos or can download from other sources.
threads_no	(int) number of threads for parallel steps (default: 8)
MetaData	Optional, List of metadata of expression matricies in same order in which expression matricies in data_list, Column number and names of all the MetaData in the list must be same
Groupby	Any column name from MetaData,which we want to use as annotation file. Only applicable if MetaData is included.
cutoff	The minimum average read counts per gene among reference cells. (The default value is 1)
Reference_name	Any one type of cell from data_id list or any one cell type from column assign to Groupby.
obs.title	Title of test/observation matrix. Default is "Observations"
ref.title	Title of reference matrix. Default is "References".
out.Filename	Store results with out.Filename prefix. Default is "inferCNV".
cluster_by_groups	If observations are defined based on groups (for example, patients), each group of cells will be clustered independently. (default = FALSE; setting k obs groups will be used)

Value

p_and_q_arm_CNV

Examples

data1 = unCTC::Poonia_et_al._PBMC_CountData
data2 = unCTC::Poonia_et_al._CountData
Data_list = list(data1,data2)
Data_Id = list("WBC","CTC")
GenePoFile = unCTC::gencode_v19_gene_pos
ref = "WBC"
path =  tempdir()
CNV_alterations(data_list=Data_list,
                data_id= Data_Id,
                min_Sample = 5,
                min_Gene = 1500,
                path=path,
                GenePositionFile=GenePoFile,
                threads_no=1,
                #MetaData=metadata,
                #Groupby=GroupID,
                Reference_name=ref,
                obs.title ="Observations",
                ref.title = "References",
                out.Filename = "inferCNV"
                )

SaritaPoonia/unCTC documentation built on Nov. 8, 2022, 12:07 p.m.