filterLowAbundanceGenes: filterLowAbundanceGenes
In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
Description
Usage
Arguments
Value
Examples
View source: R/ascend_filtering.R
Description
Removes genes if they are expressed in less than a set percentage of cells .
This step is usually done after the other filtering steps and prior to
normalisation. As this step may remove rare transcripts, this filtering step
is optional.
Usage
1
filterLowAbundanceGenes(object, pct.threshold = 1)
Arguments
object
An EMSet that has been filtered by
filterByOutliers and filterByControl.
pct.threshold
Percentage threshold as a whole number. Default: 1.
Value
An EMSet with low abundance genes removed from the
dataset.
Examples
1
2
3
4
5
# Load EMSet
raw_emset <- ascend::raw_set
# Filter low abundance genes expressed in less than 1% of cells
filtered_emset <- filterLowAbundanceGenes(raw_emset, pct.threshold = 0.1)
IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.
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Description Usage Arguments Value Examples
View source: R/ascend_filtering.R
Description
Removes genes if they are expressed in less than a set percentage of cells . This step is usually done after the other filtering steps and prior to normalisation. As this step may remove rare transcripts, this filtering step is optional.
Usage
1 | filterLowAbundanceGenes(object, pct.threshold = 1)
|
Arguments
object |
An EMSet that has been filtered by
|
pct.threshold |
Percentage threshold as a whole number. Default: 1. |
Value
An EMSet with low abundance genes removed from the dataset.
Examples
1 2 3 4 5 | # Load EMSet
raw_emset <- ascend::raw_set
# Filter low abundance genes expressed in less than 1% of cells
filtered_emset <- filterLowAbundanceGenes(raw_emset, pct.threshold = 0.1)
|
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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