megapteraPars-class: Class "megapteraPars"
In heibl/megaptera: MEGAPhylogeny Techniques in R
Description
Slots
References
See Also
Description
S4 Class for pipeline parameters of megapteraProj.
Slots
data.pathA character string giving the path to the directory there all
data and results will be stored (see megapteraInit).
gb.seq.downloadA character string defining how sequences should be
downloaded from GenBank Nucleotide; can be "eutils" or "ftp".
debug.levelNumeric, a number between 0 and 5, determining the
pipeline's verbosity. This parameter under development and should not
be changed by the user.
parallelLogical: if TRUE, several steps in the pipeline will be
run in parallel, otherwise all steps are serial.
cpusNumerical: if TRUE, several steps in the pipeline will be
run in parallel, otherwise all steps are serial.
cluster.typeA character string: if TRUE, several steps in the
pipeline will be run in parallel, otherwise all steps are serial.
update.seqsCurrently unused.
retmaxNumeric, giving the batch size when downloading sequences from
the Entrez History server (default: 500).
max.gi.per.specNumeric, giving the maximum number of sequences that
will be used per species. Can be used to avoid model organism (e.g., rice,
Drosophila, ...) cluttering up the pipeline with thousands of
sequences (default: 10).
max.bpNumeric, the maximal length of DNA sequences in base pairs to be
included in the alignment. The upper limit is determined by the alignment
program and the specific alignment and can only be determined by
trial-and-error (default: 5000).
reference.max.distCurrently unused.
min.seqs.referenceCurrently unused.
fract.missNumeric, ranging between 0 and 1. To avoid long stretches of
only a few sequences at the beginning and the ending of an alignment block
a minimum required number of sequences can be set as a fraction of the
total number of sequences in this alignment block. Has been superseeded by
the gb.* parameters.
filter1Currently unused.
filter2Currently unused.
filter3Currently unused.
filter4Currently unused.
block.max.distNumeric, ranging between 0 and 1. block.max.dist
gives the maximum genetic distance (measured as the fraction of divergent
nucleotide positions) allowed in a sequence alignment block. The alignment
of individual marker is iteratively broken into smaller blocks until this
condition is met with.
min.n.seqNumeric, the minimum number of sequences required for an
alignment block. Alignment blocks with less than min.n.seq are
dropped from the output.
max.madNumeric, giving the treshold value for the assessment of
saturation: alignments with a median average distance (MAD) of
max.mad or greater will be broken into blocks. The default value has
been estimated with simulation by Smith et al. (2009).
gb1Parameters for masking of alignment blocks with
gblocks.
gb2Parameters for masking of alignment blocks with
gblocks.
gb3Parameters for masking of alignment blocks with
gblocks.
gb4Parameters for masking of alignment blocks with
gblocks.
gb5Parameters for masking of alignment blocks with
gblocks. #' @details The pipeline's verbosity can be
fine-tuned with debug.level:
0 No progess and
diagnostic messages
1 Messages on screen
2 Messages logged
to file
3 Messages on screen and logged to file
4 Same as
3, in addition current data is saved as .rda object in case of a
foreseeable error
5 Same as 4, in addition current data is always
saved
References
Smith, S.A., J.M. Beaulieu, and M.J. Donoghue. 2009.
Mega-phylogeny approach for comparative biology: an alternative to
supertree and supermatrix approaches. BMC Evolutionary Biology
9:37.
See Also
megapteraProj for creating a megaptera project.
heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.
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Description Slots References See Also
Description
S4 Class for pipeline parameters of megapteraProj.
Slots
data.pathA character string giving the path to the directory there all data and results will be stored (see
megapteraInit).gb.seq.downloadA character string defining how sequences should be downloaded from GenBank Nucleotide; can be
"eutils"or"ftp".debug.levelNumeric, a number between 0 and 5, determining the pipeline's verbosity. This parameter under development and should not be changed by the user.
parallelLogical: if
TRUE, several steps in the pipeline will be run in parallel, otherwise all steps are serial.cpusNumerical: if
TRUE, several steps in the pipeline will be run in parallel, otherwise all steps are serial.cluster.typeA character string: if
TRUE, several steps in the pipeline will be run in parallel, otherwise all steps are serial.update.seqsCurrently unused.
retmaxNumeric, giving the batch size when downloading sequences from the Entrez History server (default: 500).
max.gi.per.specNumeric, giving the maximum number of sequences that will be used per species. Can be used to avoid model organism (e.g., rice, Drosophila, ...) cluttering up the pipeline with thousands of sequences (default: 10).
max.bpNumeric, the maximal length of DNA sequences in base pairs to be included in the alignment. The upper limit is determined by the alignment program and the specific alignment and can only be determined by trial-and-error (default: 5000).
reference.max.distCurrently unused.
min.seqs.referenceCurrently unused.
fract.missNumeric, ranging between 0 and 1. To avoid long stretches of only a few sequences at the beginning and the ending of an alignment block a minimum required number of sequences can be set as a fraction of the total number of sequences in this alignment block. Has been superseeded by the
gb.*parameters.filter1Currently unused.
filter2Currently unused.
filter3Currently unused.
filter4Currently unused.
block.max.distNumeric, ranging between 0 and 1.
block.max.distgives the maximum genetic distance (measured as the fraction of divergent nucleotide positions) allowed in a sequence alignment block. The alignment of individual marker is iteratively broken into smaller blocks until this condition is met with.min.n.seqNumeric, the minimum number of sequences required for an alignment block. Alignment blocks with less than
min.n.seqare dropped from the output.max.madNumeric, giving the treshold value for the assessment of saturation: alignments with a median average distance (MAD) of
max.mador greater will be broken into blocks. The default value has been estimated with simulation by Smith et al. (2009).gb1Parameters for masking of alignment blocks with
gblocks.gb2Parameters for masking of alignment blocks with
gblocks.gb3Parameters for masking of alignment blocks with
gblocks.gb4Parameters for masking of alignment blocks with
gblocks.gb5Parameters for masking of alignment blocks with
gblocks. #' @details The pipeline's verbosity can be fine-tuned withdebug.level:0 No progess and diagnostic messages 1 Messages on screen 2 Messages logged to file 3 Messages on screen and logged to file 4 Same as 3, in addition current data is saved as .rda object in case of a foreseeable error 5 Same as 4, in addition current data is always saved
References
Smith, S.A., J.M. Beaulieu, and M.J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9:37.
See Also
megapteraProj for creating a megaptera project.
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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