QCplots {ORFik} | R Documentation |
Correlation plots default to mRNA covering reads.
Meta plots defaults to leader, cds, trailer.
Output will be stored in same folder as the
libraries in df.
Correlation plots will be fpkm correlation and
log2(fpkm + 1) correlation between samples.
QCplots( df, region = "mrna", stats_folder = paste0(dirname(df$filepath[1]), "/QC_STATS/"), plot.ext = ".pdf", BPPARAM )
df |
an ORFik |
region |
a character (default: mrna), make raw count matrices of whole mrnas or one of (leaders, cds, trailers) |
stats_folder |
directory to save, default: paste0(dirname(df$filepath[1]), "/QC_STATS/") |
plot.ext |
character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load! |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
Is part of QCreport
invisible(NULL) (objects stored to disc)
Other QC report:
QCreport()
,
QCstats()