Description Usage Arguments Details Value See Also Examples
Load mapping statistics from log files
1 2 | loadMoiraiStats(multiplex, summary, pipeline, ercc = FALSE,
processed_data = NULL)
|
multiplex |
Optional. Path to a ‘multiplex’ file. |
summary |
Optional. Path to a ‘summary’ file. |
pipeline |
Optional. Version string identifying the pipeline used to process the data. |
ercc |
Optional. [Experimental] Return ERCC spike counts. |
processed_data |
Optional. Path to the Moirai base directory. |
Loads mapping counts and other statistics produced during processing. This
function deprecates loadLogs("moirai")
. It loads data from a summary file
and a multiplex file. When their path is not given by multiplex
and
summary
, they will be searched at fixed locations in the
PROCESSED_DATA
directory using the LIBRARY
variable (this
behaviour is deprecated and now triggers a warning).
loadMoiraiStats
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)
total Number of demultiplexed reads (if available).
extracted Number of extracted reads
cleaned Numbers of reads after removing spikes, rRNA, and other artefacts
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
Alternatively, returns ERCC spike counts when ‘ercc’ is set to ‘TRUE’.
hierarchAnnot
, loadLogs
, mapStats
Other smallCAGEqc metadata functions: llPostProcess
1 2 3 4 5 6 | libs <- loadMoiraiStats(
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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