ORFikQC {ORFik} | R Documentation

## A post Alignment quality control of reads

### Description

From this report you will get a summary csv table, with distribution of aligned reads, overlap of reads to transcript regions, like leader, cds, trailer, tRNAs, rRNAs, snoRNAs etc. It will also make you some 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. You will also get count tables over mrna, leader, cds and trailer separately, similar to HTseq count tables.

### Usage

    ORFikQC(df, out.dir = dirname(df$filepath[1]))

### Arguments

`df` | an ORFik `experiment`
`out.dir` | optional output directory, default: dirname(df$filepath[1])

### Details

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

### Value

NULL (objects stored to disc)

### Examples

    # 1. Pick directory
    dir <- system.file("extdata", "", package = "ORFik")
    # 2. Pick an experiment name
    exper <- "ORFik"
    # 3. Pick .gff/.gtf location
    txdb <- system.file("extdata", "annotations.gtf", package = "ORFik")
    template <- create.experiment(dir = dir, exper, txdb = txdb,
                                  viewTemplate = FALSE)
    template$X5[6] <- "heart" # <- fix non unique row
    # read experiment
    df <- read.experiment(template)
    # Save with: save.experiment(df, file = "path/to/save/experiment.csv")

    # ORFikQC(df)

[Package ORFik version 1.6.9 Index]