partitionReads: Cluster a SNP matrix into haplotype groups

Description Usage Arguments Value Examples

View source: R/partitionLongreads.R

Description

Cluster a SNP matrix into haplotype groups

Usage

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partitionReads(
  x,
  distAlleles = 2,
  selectAllelesBy = "count",
  threshold = 0.2,
  clMethod = "ward.D",
  minLen = 0.5,
  skipGapFreq = 0.8,
  deepSplit = 1,
  minClusterSize = 15,
  ...
)

Arguments

x

A [read x position] SNP matrix.

distAlleles

Number of distinct alleles in the sample.

threshold

Only gaps above threshold will be treated as gaps. Removes noisy positions in longreads.

clMethod

clustering method passed to hclust.

minLen

Minimal fraction of SNPs that need to be covered by a read to be used

skipGapFreq

Skip a badly behaved polymorphic position if the frequency of gaps within a haplotype group exceeds skipGapFreq.

deepSplit

sensitivity parameter passed to cutreeHybrid.

...

Additional parameters.

sortBy

sort by "distance" or "count". See partitionLongreads for details

Value

A HapPart object.

Examples

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DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.