RiboQC.plot {ORFik} | R Documentation |
Quality control for pshifted Ribo-seq data
RiboQC.plot( df, output.dir = file.path(dirname(df$filepath[1]), "QC_STATS/"), width = 6.6, height = 4.5, type = "pshifted", weight = "score", BPPARAM = BiocParallel::SerialParam(progressbar = TRUE) )
df |
an ORFik |
output.dir |
directory to save plot, default: file.path(dirname(df$filepath[1]), "QC_STATS/"). If NULL will not save. |
width |
width of plot, default 6.6 (in inches) |
height |
height of plot, default 4.5 (in inches) |
type |
type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths! |
weight |
which column in reads describe duplicates, default "score". |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
ggplot object as a grid
df <- ORFik.template.experiment() df <- df[3,] #lets only p-shift RFP sample at index 3 #shiftFootprintsByExperiment(df) #RiboQC.plot(df)