SamReads: Return a SamReads object

Description Usage Arguments Value

Description

S3 method that returns an S3 SamReads object, which is a data frame with additional meta data.

Usage

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SamReads(x, ...)

## S3 method for class 'character'
SamReads(x, source = SamSource(NULL),
  splitTags = TRUE, ...)

## S3 method for class 'Sam'
SamReads(x, ...)

## S3 method for class 'SamReads'
as.data.frame(x, ...)

Arguments

x

For the object to extract or build a sam reads object from. It can be a character vector of unparsed read lines, a Sam object, or (pretty uselessly) a SamReads object.

...

Future-proof the method. Not currently used.

source

The SamSource object to associate with the reads. If not provided and x is a Sam or SamReads object, it will default to that object's source. Otherwise the default is all missing data, i.e. SamSource(NULL)

splitTags

By default this is TRUE, meaning optional read tags are split out as named columns. Setting this FALSE leaves the optional tags as a single column, "tags", with all the extra tags presented as a single tab delimited string.

Value

A SamReads object.


jefferys/SamSeq documentation built on Oct. 25, 2019, 8:11 a.m.