filter_low_counts: Remove low count genes
In OceaneCsn/DIANE: DIANE
View source: R/fct_normalisation.R
filter_low_counts R Documentation
Remove low count genes
Description
Removes genes having a sum of counts accross all samples
lesser than the specified threshold. It returns un aupdated TCC object,
which count element contains the filtered expression matrix.
Usage
filter_low_counts(tcc, thr)
Arguments
tcc
data to be filtered to remove low count genes
thr
the sum of counts across all samples to be exceeded for a gene
Value
a TCC-Class object
Examples
data("abiotic_stresses")
tcc_object <- DIANE::normalize(abiotic_stresses$raw_counts,
abiotic_stresses$conditions, iteration = FALSE)
threshold = 10*length(abiotic_stresses$conditions)
tcc_object <- DIANE::filter_low_counts(tcc_object, threshold)
normalized_counts <- TCC::getNormalizedData(tcc_object)
OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.
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View source: R/fct_normalisation.R
| filter_low_counts | R Documentation |
Remove low count genes
Description
Removes genes having a sum of counts accross all samples lesser than the specified threshold. It returns un aupdated TCC object, which count element contains the filtered expression matrix.
Usage
filter_low_counts(tcc, thr)
Arguments
tcc |
data to be filtered to remove low count genes |
thr |
the sum of counts across all samples to be exceeded for a gene |
Value
a TCC-Class object
Examples
data("abiotic_stresses")
tcc_object <- DIANE::normalize(abiotic_stresses$raw_counts,
abiotic_stresses$conditions, iteration = FALSE)
threshold = 10*length(abiotic_stresses$conditions)
tcc_object <- DIANE::filter_low_counts(tcc_object, threshold)
normalized_counts <- TCC::getNormalizedData(tcc_object)
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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