procBam-class {casper} | R Documentation

## Class "procBam"

### 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")

[Package casper version 2.14.0 Index]