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.
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]), BPPARAM = bpparam())

### Arguments

`df` | an ORFik `experiment`
`out.dir` | optional output directory, default: `dirname(df$filepath[1])`. Will make a folder called "QC_STATS" with all results in this directory.
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`

### 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 1.10.13 Index]