constructTDS {transcriptR} | R Documentation

## constructTDS

### 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

    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

    ### Load TranscriptionDataSet object
    data(tds)

    ### View a short summary of the object
    tds

[Package transcriptR version 1.8.0 Index]