pipeline {demic}

A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration

Description

A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration

Usage

pipeline(Y, i)

Arguments

Y

a matrix of coverages

i

cutoff of filtering samples changes according to parameter i; i=1, cutoffRatio is 0.5; i=2, cutoffRatio is 1 as contig is clean

Value

a named list

• samples: final list of filtered samples

• correct_ys: dataframe with correct Y values per contig/sample

• pc1: PC1 results of PCA per contig

• pc1_range: range of PC1

• samples_y: samples filtered for reliable coverage