readFit: readFit constructor

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

readFit constructor

Description

readFit constructor

Usage

readFit(df, h, pi = NULL, position = F)

Arguments

df	read table
h	haplotype matrix
pi	haplotype frequencies, may be NULL
position	If T, assess fits based on nucleotide positions. If F, assess fits based on reads.

Details

A readFit object is a list. Each entry in the list contains the entries sampled_freq, predicted_freq, coverage, alleles, P. sampled_freq and predicted_freq are numeric vectors with an entry for each allele. Alleles is a character vector. sampled_freq always sums to 1, since alleles are those seen in the data, while predicted_freq may sum to less than 1 when a haplotype does not match any allele.

readFit objects are built based on nucleotide positions or reads. For position based readFits, the alleles are some subset of A,C,G,T which are sampled at a given position. Coverage is the number of reads that cover the position. For read based fits, the alleles are nucleotide sequences corresponding to a given sequence template (see tempate in read_table objects). Coverage is the number of reads with a given template.

Value

a readFit object

SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.