constructTDS: constructTDS

Description Usage Arguments Details Value Author(s) Examples

Description

The function constructs an object of class TranscriptionDataSet, which is a container for holding processed sequencing data and the results of all downstream analyses. All the slots of the created object are filled during the workflow by applying specific functions to the object directly.

Usage

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constructTDS(file, region, fragment.size = 250, unique = FALSE,
  paired.end = FALSE, swap.strand = FALSE, param = NULL)

Arguments

file

A path to a BAM file with sequencing reads.

region

GRanges. Genomic region(s) to extract reads from. If not supplied, all the reads from a BAM file are extracted.

fragment.size

Numeric. Extend read length to the fragment size. Default: 250.

unique

Logical. Whether to remove duplicated reads (based on the genomic coordinates). Default: FALSE.

paired.end

Logical. Whether to treat a BAM file as paired-end. Default: FALSE.

swap.strand

Logical. Whether to reverse the strand of the read. Default: FALSE.

param

ScanBamParam object influencing what fields and which records (reads) are imported from a BAM file. Default: NULL.

Details

The slots fragments, fragmentSize, region, coveragePlus, coverageMinus are filled during the object construction. The fragments holds information about genomic coordinates of the sequenced fragments (reads extended to the fragmento size). coveragePlus and coverageMinus for each position in the genome counts the number of fragments that cover it (for the details, see coverage). region holds information about the region used for fragments extraction.

Value

An object of class TranscriptionDataSet.

Author(s)

Armen R. Karapetyan

Examples

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### Load TranscriptionDataSet object
data(tds)

### View a short summary of the object
tds


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