Description Usage Arguments Details Value Author(s) See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30  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 lefthand 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 genelevel data, therefore it is not possible to guess which one to use.
A listbased object of class "hanabi".
Charles Plessy
Other CAGEr richness functions: hanabiPlot
,
plot.hanabi
1 2 3 4  h < hanabi(CTSStagCountDF(exampleCAGEexp))
h
plot(h)
hanabi(CTSStagCountGR(exampleCAGEexp, 2))

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