getOutputDataSet: Gets the (complete or incomplete) processed output data set

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Gets the (complete or incomplete) processed output data set.

Usage

 ## S3 method for class 'AromaSeqTransform'
getOutputDataSet(...)
 ## S3 method for class 'AbstractAlignment'
getOutputDataSet(this, onMissing=c("drop", "NA", "error"), ...)
 ## S3 method for class 'Bowtie2Alignment'
getOutputDataSet(this, onMissing=c("drop", "NA", "error"), ...)
 ## S3 method for class 'FastqDownsampler'
getOutputDataSet(this, ...)
 ## S3 method for class 'PicardDuplicateRemoval'
getOutputDataSet(this, onMissing=c("drop", "NA", "error"), ...)
 ## S3 method for class 'TopHat2Alignment'
getOutputDataSet(this, onMissing=c("drop", "NA", "error"), ...)
 ## S3 method for class 'TotalCnBinnedCounting'
getOutputDataSet(this, onMissing=c("drop", "NA", "error"), ...)

Arguments

onMissing	A character string specifying how non-processed files should be returned. If "drop", they are ignored and not part of the returned data set. If "dropall", NULL is returned unless all files are processed. If "NA", they are represented as a "missing" file. If "error", they are not accepted and an exception is thrown.
...	Not used.

Value

Returns the output data set containing the same number of files as the input data set, except in the case where argument onMissing is "drop" or "dropall" and one or more files is not processed.

Author(s)

Henrik Bengtsson

See Also

This method is utilized by findFilesTodo().

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.