calc_pinmat: Select features and generate the incidence table.

In seqpipe/SCclust: Clustering of Single Cell Sequencing Copy Number Profiles to Identify Clones

Description

Select features (called as pins), generate the binary matrix with rows as pins and columns as cells.

Usage

calc_pinmat(gc_df, segment_df, homoloss = 0, dropareas = NULL, smear = 1,
  chromrange = 1:24, keepboundaries = F)

Arguments

gc_df	bining schema used for the analysis
segment_df	the breakpoint table generated by segment_varbin_files.
homoloss	drop out boundary
dropareas	areas of the chromosomes that should be excluded from further analysis (e.g. centromeres)

Value

a list of pinmat and pins objects. pinmat is the incidence table; pins is the bin location

seqpipe/SCclust documentation built on May 4, 2021, 11:56 a.m.