comp_NB_residuals: Compute Negative-Binomial residuals
In VingronLab/APL: Association Plots
comp_NB_residuals R Documentation
Compute Negative-Binomial residuals
Description
Computes the residuals based on the negative binomial model. By default a
theta of 100 is used to capture technical variation.
Usage
comp_NB_residuals(mat, theta = 100, clip = FALSE, cutoff = NULL, freq = TRUE)
Arguments
mat
A numerical matrix or coercible to one by 'as.matrix()'.
Should have row and column names.
theta
Overdispersion parameter. By default set to 100 as described in
Lause and Berens, 2021 (see references).
clip
logical. Whether residuals should be clipped if they are
higher/lower than a specified cutoff
cutoff
numeric. Residuals that are larger than cutoff or lower than
-cutoff are clipped to cutoff.
freq
logical. Whether a table of frequencies (as used in CA) should
be used.
Value
A named list. The elements are:
"S": standardized residual matrix.
"tot": grand total of the original matrix.
"rowm": row masses.
"colm": column masses.
References
Lause, J., Berens, P. & Kobak, D. Analytic Pearson residuals for
normalization of single-cell RNA-seq UMI data. Genome Biol 22, 258 (2021).
https://doi.org/10.1186/s13059-021-02451-7
VingronLab/APL documentation built on Nov. 9, 2024, 5:33 p.m.
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| comp_NB_residuals | R Documentation |
Compute Negative-Binomial residuals
Description
Computes the residuals based on the negative binomial model. By default a theta of 100 is used to capture technical variation.
Usage
comp_NB_residuals(mat, theta = 100, clip = FALSE, cutoff = NULL, freq = TRUE)
Arguments
mat |
A numerical matrix or coercible to one by 'as.matrix()'. Should have row and column names. |
theta |
Overdispersion parameter. By default set to 100 as described in Lause and Berens, 2021 (see references). |
clip |
logical. Whether residuals should be clipped if they are higher/lower than a specified cutoff |
cutoff |
numeric. Residuals that are larger than cutoff or lower than -cutoff are clipped to cutoff. |
freq |
logical. Whether a table of frequencies (as used in CA) should be used. |
Value
A named list. The elements are:
"S": standardized residual matrix.
"tot": grand total of the original matrix.
"rowm": row masses.
"colm": column masses.
References
Lause, J., Berens, P. & Kobak, D. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data. Genome Biol 22, 258 (2021). https://doi.org/10.1186/s13059-021-02451-7
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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