hanabi {CAGEr} | R Documentation |
Rarefy data at multiple sample sizes using the
vegan
package and return a ‘hanabi’ object that can be passed
to plot functions.
The computation can be long, so the steps of rarefaction and plotting are kept separate.
hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'Rle' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'numeric' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'integer' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'GRanges' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'List' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'list' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'matrix' hanabi( x, n = 20, step = 0.75, from = NULL, useMulticore = FALSE, nrCores = NULL )
x |
An object contained expression counts on which richness scores can
be calculated. For example an expression table in |
n |
The maximum number of rarefactions per sample. |
step |
Subsample sizes are calculated by taking the largest sample and multiplying it by the step "n" times. |
from |
Add one sample size (typically "0") in order to extend the plot on the left-hand side. |
useMulticore |
Logical, should multicore be used.
|
nrCores |
Number of cores to use when |
This function does not take directly CAGEr objects as input, because hanabi plots can be made from CTSS, clustered or gene-level data, therefore it is not possible to guess which one to use.
A list-based object of class "hanabi".
Charles Plessy
vegan::rarecurve
.
Other CAGEr richness functions:
hanabiPlot()
,
plot.hanabi()
h <- hanabi(CTSStagCountDF(exampleCAGEexp)) h plot(h) hanabi(CTSStagCountGR(exampleCAGEexp, 2))