QCreport {ORFik} | R Documentation

## A post Alignment quality control of reads

### Description

The ORFik QC uses the aligned files (usually bam files), fastp and STAR log files combined with annotation to create relevant statistics.
This report consists of several steps:
1. Convert bam file / Input files to ".ofst" format, if not already done. This format is around 400x faster to use in R than the bam format. Files are also outputted to R environment specified by `envExp(df)`
2. From this report you will get a summary csv table, with distribution of aligned reads and overlap counts over transcript regions like: leader, cds, trailer, lincRNAs, tRNAs, rRNAs, snoRNAs etc. It will be called STATS.csv. And can be imported with `QCstats` function.
3. It will also make correlation plots and meta coverage plots, so you get a good understanding of how good the quality of your NGS data production + aligner step were.
4. Count tables are produced, similar to HTseq count tables. Over mrna, leader, cds and trailer separately. This tables are stored as `SummarizedExperiment`, for easy loading into DEseq, conversion to normalized fpkm values, or collapsing replicates in an experiment. And can be imported with `countTable` function.
Everything will be outputed in the directory of your NGS data, inside the folder ./QC_STATS/, relative to data location in 'df'. You can specify new out location with out.dir if you want.
To make a ORFik experiment, see ?ORFik::experiment
To see some normal mrna coverage profiles of different RNA-seq protocols: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310221/figure/F6/

### Usage

    QCreport(
      df,
      out.dir = dirname(df$filepath[1]),
      plot.ext = ".pdf",
      create.ofst = TRUE,
      complex.correlation.plots = TRUE,
      BPPARAM = bpparam()
    )

### Arguments

`df` | an ORFik `experiment`
`out.dir` | optional output directory, default: `dirname(df$filepath[1])`. Will make a folder called "QC_STATS" with all results in this directory. Warning: If you assign not default path, you will have a hazzle to load files later. Much easier to load count tables, statistics, ++ later with default.
`plot.ext` | character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!
`create.ofst` | logical, default TRUE. Create ".ofst" files from the input libraries, ofst is much faster to load in R, for later use. Stored in ./ofst/ folder relative to experiment main folder.
`complex.correlation.plots` | logical, default TRUE. Add in addition to simple correlation plot two computationally heavy dots + correlation plots. Useful for deeper analysis, but takes longer time to run, especially on low-quality gpu computers. Set to FALSE to skip these.
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`. You can also add a time remaining bar, for a more detailed pipeline.

### Value

invisible(NULL) (objects are stored to disc)

### See Also

Other QC report: `QCplots()`, `QCstats()`

### Examples

    # Load an experiment
    df <- ORFik.template.experiment()
    # Run QC
    # QCreport(df)

[Package ORFik version 1.14.7 Index]