partitionReads: Cluster a SNP matrix into haplotype groups
In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description Usage Arguments Value Examples

Cluster a SNP matrix into haplotype groups

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

`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