ORFikQC {ORFik} | R Documentation |
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.
ORFikQC(df, out.dir = dirname(df$filepath[1]))
df |
an ORFik |
out.dir |
optional output directory, default: dirname(df$filepath[1]) |
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
NULL (objects stored to disc)
# 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)