Description Usage Arguments Details Value
Returns a parameter list with default parameter values.
1 2 3 4 | parameters(wd = ".", txid = character(), mkblstdb = "", blstn = "",
v = FALSE, ncps = 1, mxnds = 1e+05, mdlthrs = 3000, mnsql = 250,
mxsql = 2000, mxrtry = 100, mxsqs = 50000, mxevl = 1e-10,
mncvrg = 51, btchsz = 100, date = Sys.Date())
|
wd |
The working directory where all output files are saved. |
txid |
Taxonomic group of interest, allows vectors. |
mkblstdb |
File path to makeblastdb |
blstn |
File path to blastn |
v |
Print progress statements to console? Statements will always be printed to log.txt. |
ncps |
The number of threads to use in the local-alignment search tool. |
mxnds |
The maximum number of nodes descending from a taxonomic group. If there are more than this number, nodes at the lower taxonomic level are analysed. |
mdlthrs |
'Model organism threshold'. Taxa with more sequences than this number will be considered model organisms and a random mdlthrs subset of their sequences will be downloaded. |
mnsql |
The minimum length of sequence in nucleotide base pairs to download. |
mxsql |
The maximum length of sequence in nucleotide base pairs to download. Any longer sequences will be ignored. |
mxrtry |
The maximum number of attempts to make when downloading. |
mxsqs |
The maximum number of sequences to BLAST in all-vs-all searches. If there are more sequences for a node, BLAST is performed at the lower taxonomic level. |
mxevl |
The maximum E-value for a successful BLAST. |
mncvrg |
The maximum percentile coverage defining an overlapping BLAST hit. Sequences with BLAST matches with lower values are not considered orthologous. |
btchsz |
Batch size when querying NCBI |
date |
Date when pipeline was initiated |
This function is NOT used to change the parameters in a folder. Use parameters_reset() instead. The purpose of this function is to describe the paramaters and present their default values.
list
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