readConfig: Read in a config file (preferred method)
In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses
Description
Usage
Arguments
Details
Value
Description
This function parses config file to extract data needed to create a FASTQ2OTU class object. It assumes that
the file is in YML format and contains default key terms.
Execute getSlots("fastq2otu") to get all required arguments or refer to documenation for more details and/or
examples.
Usage
1
readConfig(configFile, isPaired = FALSE, type = c("auto"))
Arguments
configFile
Path to config file (YML-formatted)
isPaired
Default is FALSE. If TRUE, parameters for paired-end data will be used.
type
Default is 'auto'. String or vector containing the following value(s): 'auto', 'assignTax', 'report', 'seqdump', 'primertrim', 'filter', 'qualityplot'. Used to specify what type of object is being created.
If a vector is provided it must contain one of the following combination of strings c('auto', 'assignTax') and c('auto', 'filter')
Details
Use when config file is supplied and all required values are provided.
Value
An S4 object
ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.
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.
Description Usage Arguments Details Value
Description
This function parses config file to extract data needed to create a FASTQ2OTU class object. It assumes that the file is in YML format and contains default key terms. Execute getSlots("fastq2otu") to get all required arguments or refer to documenation for more details and/or examples.
Usage
1 | readConfig(configFile, isPaired = FALSE, type = c("auto"))
|
Arguments
configFile |
Path to config file (YML-formatted) |
isPaired |
Default is FALSE. If TRUE, parameters for paired-end data will be used. |
type |
Default is 'auto'. String or vector containing the following value(s): 'auto', 'assignTax', 'report', 'seqdump', 'primertrim', 'filter', 'qualityplot'. Used to specify what type of object is being created. If a vector is provided it must contain one of the following combination of strings c('auto', 'assignTax') and c('auto', 'filter') |
Details
Use when config file is supplied and all required values are provided.
Value
An S4 object
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.