Transfer a copy of microhaplot app.
Description
Moves shiny microhaplot app to a different directory
Usage
mvShinyHaplot(path)
Arguments
path
string. directory path. Required
Value
a logical value of whether file.copy is successfully transferred Shiny app to its new directory
Examples
mvShinyHaplot(tempdir())
Extracts haplotype from alignment reads.
Description
The function microhaplot extracts haplotype from sequence alignment files through perl script hapture and returns a summary table of the read depth and read quality associate with haplotype.
Usage
prepHaplotFiles(run.label, sam.path, label.path, vcf.path,
out.path = tempdir(), add.filter = FALSE, app.path = tempdir(),
n.jobs = 1)
Arguments
run.label
character vector. Run label to be used to display in haPLOType. Required
sam.path
string. Directory path folder containing all sequence alignment files (SAM). Required
label.path
string. Label file path. This customized label file is a tab-separate file that contains entries of SAM file name, individual ID, and group label. Required
vcf.path
string. VCF file path. Required
out.path
string. Optional. If not specified, the intermediate files are created under TEMPDIR, with the assumption that directory is granted for written permission.
add.filter
boolean. Optional. If true, this removes any haplotype with unknown and deletion alignment characters i.e. "*" and "_", removes any locus with large number of haplotypes ( # > 40) , and remove any locus with fewer than half of the total individuals.
app.path
string. Path to shiny haPLOType app. Optional. If not specified, the path is default to TEMPDIR.
n.jobs
positive integer. Number of SAM files to be parallel processed. Optional. This multithread is only available for non Window OS. Recommend two times the number of processors/core.
Value
This function returns a dataframe of 9 columns i.e group, id, locus, haplotype, depth, sum of Phred score, max of Phred score, allele balance and haplotype rank from highest to lowest read depth. This dataframe will also be saved in out.path.
Examples
run.label <- "sebastes"
sam.path <- tempdir()
untar(system.file("extdata",
"sebastes_sam.tar.gz",
package="microhaplot"),
exdir = sam.path)
label.path <- file.path(sam.path, "label.txt")
vcf.path <- file.path(sam.path, "sebastes.vcf")
mvShinyHaplot(tempdir())
app.path <- file.path(tempdir(), "microhaplot")
# retrieve system Perl version number
perl.version <- as.numeric(system('perl -e "print $];"', intern=TRUE))
if (perl.version >= 5.014) {
haplo.read.tbl <- prepHaplotFiles(run.label = run.label,
sam.path = sam.path,
out.path = tempdir(),
label.path = label.path,
vcf.path = vcf.path,
app.path = app.path)
}else {
message("Perl version is outdated. Must >= 5.014.")}
Run shiny microhaplot
Description
Run shiny microhaplot app
Usage
runShinyHaplot(path = system.file("shiny", "microhaplot", package =
"microhaplot"))
Arguments
path
Path to shiny microhaplot app. Optional. If not specified, the path is default to local app path.
Value
Runs shiny microhaplot application via shiny::runApp which typically doesn't return; interrupt R to stop the application (usually by pressing Ctrl+C or Esc).
Examples
if(interactive()){
runShinyHaplot()
}