| Name : R-SRS
| |
| Version : 0.2.3
| Vendor : obs://build_opensuse_org/devel:languages:R
|
| Release : lp153.12.2
| Date : 2024-06-14 12:03:52
|
| Group : Development/Libraries/Other
| Source RPM : R-SRS-0.2.3-lp153.12.2.src.rpm
|
| Size : 0.06 MB
| |
| Packager : (none)
| |
| Summary : Scaling with Ranked Subsampling
|
Description :
Analysis of species count data in ecology often requires normalization
to an identical sample size. Rarefying (random subsampling without
replacement), which is a popular method for normalization, has been
widely criticized for its poor reproducibility and potential distortion
of the community structure. In the context of microbiome count data,
researchers explicitly advised against the use of rarefying. An
alternative to rarefying is scaling with ranked subsampling (SRS). SRS
consists of two steps. In the first step, the total counts for all OTUs
(operational taxonomic units) or species in each sample are divided by
a scaling factor chosen in such a way that the sum of the scaled counts
Cscaled equals Cmin. In the second step, the non-integer Cscaled values
are converted into integers by an algorithm that we dub ranked
subsampling. The Cscaled value for each OTU or species is split into
the integer part Cint (Cint = floor(Cscaled)) and the fractional part
Cfrac (Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or
equal to Cmin, additional delta C = Cmin - the sum of Cint counts have
to be added to the library to reach the total count of Cmin. This is
achieved as follows. OTUs are ranked in the descending order of their
Cfrac values. Beginning with the OTU of the highest rank, single count
per OTU is added to the normalized library until the total number of
added counts reaches delta C and the sum of all counts in the
normalized library equals Cmin. When the lowest Cfrag involved in
picking delta C counts is shared by several OTUs, the OTUs used for
adding a single count to the library are selected in the order of their
Cint values. This selection minimizes the effect of normalization on
the relative frequencies of OTUs. OTUs with identical Cfrag as well as
Cint are sampled randomly without replacement. See Beule & Karlovsky
(2020) < doi:10.7717/peerj.9593> for details.
|
RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Leap_15.3/x86_64 |
