calculate_matrix_stats: calculate_matrix_stats(countmatrix = NULL, uselog = NULL,...
In johnmcculloch/JAMS_BW: Just A Microbiology System
View source: R/calculate_matrix_stats.R
calculate_matrix_stats R Documentation
calculate_matrix_stats(countmatrix = NULL, uselog = NULL, statsonlog = TRUE, stattype = NULL, classesdf = NULL, invertbinaryorder = FALSE, fun_for_l2fc = "geom_mean", threshPA = 0, numthreads = 1, nperm = 10000, paired = FALSE)
Description
Returns a data frame with the statistics for a feature count matrix ordered by highest variance or lowest Mann-Whitney-Wilcoxon test between binary categories.
This function is used internally by the JAMS plotting functions, plot_Ordination, plot_relabund_heatmap, plot_correlation_heatmpap and plot_relabund_features.
Usage
calculate_matrix_stats(
countmatrix = NULL,
uselog = NULL,
statsonlog = TRUE,
stattype = NULL,
classesdf = NULL,
invertbinaryorder = FALSE,
fun_for_l2fc = "geom_mean",
threshPA = 0,
numthreads = 1,
nperm = 10000,
paired = FALSE
)
johnmcculloch/JAMS_BW documentation built on Jan. 6, 2025, 5:14 a.m.
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View source: R/calculate_matrix_stats.R
| calculate_matrix_stats | R Documentation |
calculate_matrix_stats(countmatrix = NULL, uselog = NULL, statsonlog = TRUE, stattype = NULL, classesdf = NULL, invertbinaryorder = FALSE, fun_for_l2fc = "geom_mean", threshPA = 0, numthreads = 1, nperm = 10000, paired = FALSE)
Description
Returns a data frame with the statistics for a feature count matrix ordered by highest variance or lowest Mann-Whitney-Wilcoxon test between binary categories. This function is used internally by the JAMS plotting functions, plot_Ordination, plot_relabund_heatmap, plot_correlation_heatmpap and plot_relabund_features.
Usage
calculate_matrix_stats(
countmatrix = NULL,
uselog = NULL,
statsonlog = TRUE,
stattype = NULL,
classesdf = NULL,
invertbinaryorder = FALSE,
fun_for_l2fc = "geom_mean",
threshPA = 0,
numthreads = 1,
nperm = 10000,
paired = FALSE
)
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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