Imports NGS-related log files such as those generated from stderr \lifecyclematuring
Which element of the parsed object to return. Ignored in all
file types except when
logical(1). Remove paths from the Filename column
Imports one or more log files as output by tools such as:
autoDetect can be used to detect the log type by parsing the file.
The featureCounts log file corresponds to the
not the main
Whilst most log files return a single tibble, some are more complex with multiple modules.
adapterRemoval can return one of four modules (which = 1:4),.
When calling by name, the possible values are sequences, settings,
statistics or distribution.
Partial matching is implemented.
cutadapt can return one of five modules (which = 1:5).
When calling by name the possible modules are summary, adapter1, adapter2,
adapter3 or overview.
Note that adapter2/3 may be missing from these files depending on the nature
of your data.
If cutadapt log files are obtained using
report=minimal, all supplied
log files must be of this format and no modules can be returned.
duplicationMetrics will return either the metrics of histogram.
These can be requested by setting which as 1 or 2, or naming either module.
Column names are broadly similar to the text in supplied files,
but have been modified for easier handling under R naming conventions.
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