Load mapping statistics from log files
Indicate to load the data from log files in the current directory, or from the summary file of Moirai.
Optional. Path to a ‘multiplex’ file.
Optional. Path to a ‘summary’ file.
Optional. Version string identifying the pipeline used to process the data.
Loads mapping counts and other statistics produced during processing.
loadLogs will load data from every file
ending in sQuote
.log in the work directory. Thes files are expected
contain tab-separated triples, with first the name of the mapping statistics,
like extracted, mapped, rdna, etc., then the sample identifier, and then the
number of reads.
loadLogs will crash or produce incorrect output if the
files do not contain triples, or if the sample identifiers are not matched
correctly in the files, or if the first word of the triples appears in multiple
loadLogs will load data from a summary file
and a multiplex file. When their path is not given by
summary, they will be searched at fixed locations in the
PROCESSED_DATA directory using the
loadLogs will recognise the ‘nano-fluidigm’
or the ‘nanoCAGE2’ Moirai users, or fail. For the ‘nano-fluidigm’
user, the samples are sorted by numbers and associated to sorted well names, from
A01, A02, ..., to H11 and H12.
Returns a data frame with one row per sample, and the following columns (if the corresponding data is available).
samplename Sample identifier (factor)
extracted Number of extracted reads
tagdust Number of reads containing oligonucleotide artefacts
spikes Number of reads overlaping with the reference spike sequences
rdna Number of reads overlaping with the reference ribosomal DNA sequences
mapped Number of reads aligned to the reference genome
1 2 3 4 5 6
loadLogs( "moirai" , summary = system.file("extdata/summary.txt", package="smallCAGEqc") , multiplex = system.file("extdata/samplename_to_sampleid.txt", package="smallCAGEqc") , pipeline="OP-WORKFLOW-CAGEscan-short-reads-v2.0") libs$group <- libs$samplename %>% sub("Run._", "", .) %>% substr(1,1) %>% factor
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