HapPart: HapPart (Haplotype Partition) stores the haplotype...

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

HapPart (Haplotype Partition) stores the haplotype information from longread clustering.

Usage

HapPart(readNames, snpPos)

## S3 method for class 'HapPart'
mcoef(x)

## S3 method for class 'HapPart'
PWM(x)

## S3 method for class 'HapPart'
OC(x)

## S3 method for class 'HapPart'
SCR(x)

## S3 method for class 'HapPart'
K(x)

## S3 method for class 'HapPart'
SQS(x)

## S3 method for class 'HapPart'
CLS(x)

## S3 method for class 'HapPart'
SNP(x)

## S3 method for class 'HapPart'
PRT(x)

## S3 method for class 'HapPart'
HTR(x)

Arguments

readNames	The names of reads in each cluster.
snpPos	SNP positions used for clustering.
x	A HapPart object.

Value

HapPart object.

Methods (by generic)

• mcoef: The membership coefficient in the assigned clade.

• PWM: Get the Position Weight Matrix

• OC: The original clusters from hclust.

• SCR: The membership scores for each read in each cluster.

• K: The total number of polymorphic positions used.

• SQS: Get the consensus sequences of the haplotypes.

• CLS: Get the classification of the haplotype partitioning.

• SNP: Get the SNP positions.

• PRT: The haplotype assignment as a character vector <A>, <B>, ... for each read.

• HTR: The cluster tree produced by hclust.

Slots

readNames

The names of reads in each cluster.

snpPos

SNP positions used for clustering.

mcoef

membership coefficient. Score for each read for belonging to its cluster. Based on the sum of probabilities of a PWM of the haplotype sequences.

tree

The resulting tree from hclust.

scores

The same scores as in mcoef, but for all clusters.

mats

PWM matrices of the haplotype sequences.

classification

... TODO

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