readLengthTable: Make table of readlengths
In Roleren/ORFik: Open Reading Frames in Genomics
View source: R/report_helpers.R
readLengthTable R Documentation
Make table of readlengths
Description
Summarizing all libraries in experiment,
make a table of proportion of read lengths.
Usage
readLengthTable(df, output.dir = NULL, type = "ofst", BPPARAM = bpparam())
Arguments
df
an ORFik experiment
output.dir
NULL or character path, default: NULL, plot not saved to disc.
If defined saves plot to that directory with the name "./readLengths.csv".
type
character, default: "ofst". Type of library:
either "default", usually bam format (the one you gave to experiment),
"pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig"
BPPARAM
a core param, default: single thread: BiocParallel::SerialParam().
Set to BiocParallel::bpparam() to use multicore. Be aware, this uses a lot of
extra ram (40GB+) for larger human samples!
Value
a data.table object of the the read length data with columns:
c("sample", "sample_id", "read length", "counts",
"counts_per_sample", "perc_of_counts_per_sample")
Roleren/ORFik documentation built on April 25, 2024, 8:41 p.m.
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View source: R/report_helpers.R
| readLengthTable | R Documentation |
Make table of readlengths
Description
Summarizing all libraries in experiment, make a table of proportion of read lengths.
Usage
readLengthTable(df, output.dir = NULL, type = "ofst", BPPARAM = bpparam())
Arguments
df |
an ORFik |
output.dir |
NULL or character path, default: NULL, plot not saved to disc. If defined saves plot to that directory with the name "./readLengths.csv". |
type |
character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig" |
BPPARAM |
a core param, default: single thread: |
Value
a data.table object of the the read length data with columns:
c("sample", "sample_id", "read length", "counts",
"counts_per_sample", "perc_of_counts_per_sample")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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