View source: R/report_helpers.R
QC_count_tables | R Documentation |
The better the annotation / gtf used, the more results you get.
QC_count_tables(
df,
out.dir,
type = "ofst",
use_simplified_reads = TRUE,
force = TRUE,
library.names = bamVarName(df),
BPPARAM = bpparam()
)
df |
an ORFik |
out.dir |
character, output directory, default:
|
type |
a character(default: "default"), load files in experiment
or some precomputed variant, like "ofst" or "pshifted".
These are made with ORFik:::convertLibs(),
shiftFootprintsByExperiment(), etc.
Can also be custom user made folders inside the experiments bam folder.
It acts in a recursive manner with priority: If you state "pshifted",
but it does not exist, it checks "ofst". If no .ofst files, it uses
"default", which always must exists. |
use_simplified_reads |
logical, default TRUE. For count tables and coverage plots a speed up for GAlignments is to use 5' ends only. This will lose some detail for splice sites, but is usually irrelevant. Note: If reads are precollapsed GRanges, set to FALSE to avoid recollapsing. |
force |
logical, default TRUE If TRUE, reload library files even if
matching named variables are found in environment used by experiment
(see |
library.names |
character vector, names of libraries, default: name_decider(df, naming) |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
a data.table of the count info
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