Report: Report
In elmerfer/RMiXCR: An easy wrapper for MiXCR software
View source: R/RMiXCR_reports.R
Report R Documentation
Report
Description
In order to export alignment results or clones from a binary file (.clns) to a human-readable tab or excel file
Usage
Report(clonsFile, type = c("full","min"), otherFields, fileType = c("Excel","tab"))
Arguments
clonsFile
the full path to the clone file (subjsect.R1.fastq.clones.clns) as returned by RunMiXCRseqClones
type
string "full" (default) or "min"
otherFields
other fields (not implemented yet)
fileType
Excel or tab (tab delimited)
Details
The resulting tab-delimited text file or excel file (type param) will contain columns with different types of information.
If no options are specified (otherFields), the default set of columns - which is sufficient in most cases - will be exported.
The possible columns include. See details in [MiXCR main page](https://mixcr.readthedocs.io/en/master/export.html):
aligned sequences, qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene region present in sequence, etc. When exporting clones, the additional columns include: clone count, clone fraction etc.
One can customize the list of fields that will be exported by passing parameters to export commands (not implemented yet).
elmerfer/RMiXCR documentation built on May 27, 2023, 5:08 a.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.
View source: R/RMiXCR_reports.R
| Report | R Documentation |
Report
Description
In order to export alignment results or clones from a binary file (.clns) to a human-readable tab or excel file
Usage
Report(clonsFile, type = c("full","min"), otherFields, fileType = c("Excel","tab"))
Arguments
clonsFile |
the full path to the clone file (subjsect.R1.fastq.clones.clns) as returned by |
type |
string "full" (default) or "min" |
otherFields |
other fields (not implemented yet) |
fileType |
Excel or tab (tab delimited) |
Details
The resulting tab-delimited text file or excel file (type param) will contain columns with different types of information. If no options are specified (otherFields), the default set of columns - which is sufficient in most cases - will be exported. The possible columns include. See details in [MiXCR main page](https://mixcr.readthedocs.io/en/master/export.html): aligned sequences, qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene region present in sequence, etc. When exporting clones, the additional columns include: clone count, clone fraction etc. One can customize the list of fields that will be exported by passing parameters to export commands (not implemented yet).
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.