loadMoiraiStats: loadMoiraiStats

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Load mapping statistics from log files

Usage

loadMoiraiStats(multiplex, summary, pipeline, ercc = FALSE,
  processed_data = NULL)

Arguments

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.

Details

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.

Value

Returns a data frame with one row per sample, and the following columns (if the corresponding data is available).

1. samplename Sample identifier (factor)

2. total Number of demultiplexed reads (if available).

3. extracted Number of extracted reads

4. cleaned Numbers of reads after removing spikes, rRNA, and other artefacts

5. tagdust Number of reads containing oligonucleotide artefacts

6. spikes Number of reads overlaping with the reference spike sequences

7. rdna Number of reads overlaping with the reference ribosomal DNA sequences

8. mapped Number of reads aligned to the reference genome

Alternatively, returns ERCC spike counts when ‘ercc’ is set to ‘TRUE’.

See Also

hierarchAnnot, loadLogs, mapStats

Other smallCAGEqc metadata functions: llPostProcess

Examples

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

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.