procBam-class: Class "procBam"

In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description

Stores processed bam files in a RangedData format. Each read is split into disjoint ranges according to its cigar code.

Objects from the Class

Objects are created with a call to procBam.

Slots

pbam

GRanges indicating chromosome, start and end of each disjoint range. The pair id and read id within the pair are also stored.

junx

GRanges indicating chromosome, start and end of junctions spanned by reads.

stranded

Logical variable. TRUE indicates that the reads were obtained from and RNA-seq experiment where strand information was preserved.

In the case of stranded experiments:

plus

GRanges indicating chromosome, start and end of each disjoint range for fragments originated from the positive strand. The pair id and read id within the pair are also stored.

minus

GRanges indicating chromosome, start and end of each disjoint range for fragments originated from the negative strand. The pair id and read id within the pair are also stored.

pjunx

GRanges indicating chromosome, start and end of junctions spanned by reads originated from the positive strand.

mjunx

GRanges indicating chromosome, start and end of junctions spanned by reads originated from the negative strand.

Methods

show

signature(object = "procBam"): Displays general information about the object.

getReads

signature(x = "procBam"): Extracts the aligned reads stored in x.

Author(s)

Camille Stephan-Otto Attolini, David Rossell

See Also

getReads

Examples

showClass("procBam")

casper documentation built on Dec. 17, 2020, 2:01 a.m.