control_window_normalise: performs control window based normalisation of the selected...
In TeamMacLean/atacr: Analysing Capture Seq Count Data
Description
Usage
Arguments
Value
Description
performs control window based normalisation of the selected set of windows, calculates a median virtual experiment and normalises to that
Usage
1
2
control_window_normalise(data, window_file, which = "bait_windows",
by_treatment = FALSE)
Arguments
data
a list of SummarizedExperiment objects from atacr::make_counts()
window_file
a text file containing the positions of control window/gene ranges
which
the subdivision of the genome to calculate correlations either 'whole_genome', 'bait_windows' or 'non_bait_windows'
by_treatment
should normalisation be done by all experiments (one median virtualexperiment to compare all samples to) OR should normalisation be done by each treatment type (one median virtual experiment for each different treatment type)
Value
a vector of scaling factors from control genes
TeamMacLean/atacr documentation built on May 9, 2019, 4:24 p.m.
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Description Usage Arguments Value
Description
performs control window based normalisation of the selected set of windows, calculates a median virtual experiment and normalises to that
Usage
1 2 | control_window_normalise(data, window_file, which = "bait_windows",
by_treatment = FALSE)
|
Arguments
data |
a list of SummarizedExperiment objects from atacr::make_counts() |
window_file |
a text file containing the positions of control window/gene ranges |
which |
the subdivision of the genome to calculate correlations either 'whole_genome', 'bait_windows' or 'non_bait_windows' |
by_treatment |
should normalisation be done by all experiments (one median virtualexperiment to compare all samples to) OR should normalisation be done by each treatment type (one median virtual experiment for each different treatment type) |
Value
a vector of scaling factors from control genes
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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