getdirectory: Common helper functions for WADE analysis December 21 2023,...
In phac-nml/wade: Executes molecular typing on contig assemblies
View source: R/CommonFunctions.R
getdirectory R Documentation
Common helper functions for WADE analysis
December 21 2023, Shelley Peterson
Description
Common helper functions for WADE analysis
December 21 2023, Shelley Peterson
Usage
getdirectory(curr_work_dir, Org_id, Test_id)
Arguments
curr_work_dir
Start up directory from pipeline project to locate system file structure
Org_id
Organism to query: GAS, PNEUMO or GONO
Test_id
AMR, TOXINS, VIRULENCE, NGSTAR, use MASTER for 16S id
SampleNo
Sample number associated with contig.fasta file
LocusID
The locus to query, or enter "list" to use a list of alleles
directorylist
the list generated from the getdirectory function
SampleList.df
the list of samples being used
reflist
the list generated from the refdirectory function
NumLoci
the number of loci being analyzed
LocusList.df
the list of loci being analyzed
Blast_evalue
the evalue parameter for the Blast function
CurrLocus
the current locus being analyzed
LocusFile
the location for the reference locus file
blastoutput
the BLAST output file to be parsed
Details
These are helper functions to streamline the other WADE functions
Value
a dataframe or list to be fed into other WADE functions
phac-nml/wade documentation built on March 16, 2024, 8:32 a.m.
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View source: R/CommonFunctions.R
| getdirectory | R Documentation |
Common helper functions for WADE analysis December 21 2023, Shelley Peterson
Description
Common helper functions for WADE analysis December 21 2023, Shelley Peterson
Usage
getdirectory(curr_work_dir, Org_id, Test_id)
Arguments
curr_work_dir |
Start up directory from pipeline project to locate system file structure |
Org_id |
Organism to query: GAS, PNEUMO or GONO |
Test_id |
AMR, TOXINS, VIRULENCE, NGSTAR, use MASTER for 16S id |
SampleNo |
Sample number associated with contig.fasta file |
LocusID |
The locus to query, or enter "list" to use a list of alleles |
directorylist |
the list generated from the getdirectory function |
SampleList.df |
the list of samples being used |
reflist |
the list generated from the refdirectory function |
NumLoci |
the number of loci being analyzed |
LocusList.df |
the list of loci being analyzed |
Blast_evalue |
the evalue parameter for the Blast function |
CurrLocus |
the current locus being analyzed |
LocusFile |
the location for the reference locus file |
blastoutput |
the BLAST output file to be parsed |
Details
These are helper functions to streamline the other WADE functions
Value
a dataframe or list to be fed into other WADE functions
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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