scm_which_downsamp_n: Determine recommended downsampling depth.
In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data
scm_which_downsamp_n R Documentation
Determine recommended downsampling depth.
Description
If the parameter scm_n_downsamp is set, it will be returned. If it is null, we return the 5th percentile of the umi count or 750, depending which is larger. However, if the median umi count is lower than this, we use it as the depth. In usch "bad" cases, it may be a good idea to tune the parameter after looking at the umi distribution and resolving possibilities for empty wells/barcodes
Usage
scm_which_downsamp_n(scmat)
Arguments
mat_id
tanaylab/metacell documentation built on Oct. 19, 2023, 1:01 p.m.
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| scm_which_downsamp_n | R Documentation |
Determine recommended downsampling depth.
Description
If the parameter scm_n_downsamp is set, it will be returned. If it is null, we return the 5th percentile of the umi count or 750, depending which is larger. However, if the median umi count is lower than this, we use it as the depth. In usch "bad" cases, it may be a good idea to tune the parameter after looking at the umi distribution and resolving possibilities for empty wells/barcodes
Usage
scm_which_downsamp_n(scmat)
Arguments
mat_id |
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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