addSeqPref: Add sequence preference to qseaSet object

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Add sequence preference to qseaSet object

Description

This function allows to add window specific sequencing preference, that can be used by the normalization procedure. This preference can be defined by the user, or estimated from sequencing of input libraries.

Usage

addSeqPref(qs, seqPref,file_name, fragment_length, paired=FALSE, 
uniquePos=TRUE, alpha=0.05, pseudocount=5, cut=3)

Arguments

qs	a qseaSet object
seqPref	A vector with predefined sequencing preference for each window. Values are interpreted as log2 ratios relative to normal/average sequencing preference.
file_name	alternatively, the sequencing preference can be estimated from input sequencing. In this case, provide the column of the sample table that contains the file names for input sequencing alignment or coverage files.
fragment_length	for single end data, provide the expected fragment length
paired	if set to TRUE, data is considered to be paired end sequencing, and the actual fragments size is used.
uniquePos	if set to TRUE, fragments with same position and orientation are considered to be PCR duplicates and replaced by one representative.
alpha	currently ignored
pseudocount	this value is added to the coverage of each window, to smooth the estimates.
cut	absolute log2 value threshold for windows to be excluded from later analysis due to extreme preference values.

Value

the function returns the qseaSet object, extended by the sequencing preference for all genomic windows.

Author(s)

Mathias Lienhard

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.