| Title: | Interactive graphical application for clinical assessment of sequence coverage at the base-pair level |
|---|---|
| Description: | a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name. |
| Authors: | Emanuela Iovino [cre, aut], Tommaso Pippucci [aut] |
| Maintainer: | Emanuela Iovino <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.15.0 |
| Built: | 2024-07-11 05:33:12 UTC |
| Source: | https://github.com/bioc/uncoverappLib |
wrapper function for getting BiocFileCache associated with uncoverapp package wrapper function for getting BiocFileCache associated with uncoverapp package
.get_cache().get_cache()
BiocFileCache object associated with uncoverappLib
Function to build input file for unCOVERAPP when the number of genes to analyze is > 50.
buildInput( geneList, genome, type_bam, bamList, outDir, type_input, MAPQ.min = 1, base.quality = 1 )buildInput( geneList, genome, type_bam, bamList, outDir, type_input, MAPQ.min = 1, base.quality = 1 )
geneList |
a text file, named with .txt extension, containing HGNC official gene name(s) one per row. |
genome |
(char) reference genome, hg19 or hg38 |
type_bam |
(char) chromosome notation of their BAM file(s). Use "number" or "chr". In the BAM file, the number option refers to 1, 2, ..., X,.M chromosome notation, while the chr option refers to chr1, chr2, ... chrX, chrM chromosome notation. |
bamList |
a text file, named with .list extension, containing the absolute paths to BAM file(s) one per row. |
outDir |
(char) directory where pileup output will be stored |
type_input |
(char) type of input target. Use "target" or "genes". If you use a list of gene names use "genes", if you use a target bed use "target". |
MAPQ.min |
(integer) minimum MAPQ value for an alignment to be included in output file. |
base.quality |
(integer) minimum QUAL value for each nucleotide in an alignment. |
Two file: a file.bed containing tab-separated specifications of genomic coordinates (chromosome, start position, end position), the coverage value, and the reference:alternate allele counts for each position and a file.txt with statistical summary of coverage
gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib") bam_example <- system.file("extdata", "example_POLG.bam", package = "uncoverappLib") cat(bam_example, file = "bam.list", sep = "\n") temp_dir=tempdir() buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr", bamList= "bam.list",type_input="genes", outDir= temp_dir)gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib") bam_example <- system.file("extdata", "example_POLG.bam", package = "uncoverappLib") cat(bam_example, file = "bam.list", sep = "\n") temp_dir=tempdir() buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr", bamList= "bam.list",type_input="genes", outDir= temp_dir)
download and rename sorted.bed.gz and sorted.bed.gz.tbi files for annotation of low-coverage positions.
getAnnotationFiles(verbose = FALSE, vignette = FALSE)getAnnotationFiles(verbose = FALSE, vignette = FALSE)
verbose |
(logical) print messages |
vignette |
(logical) download example annotation-file in vignette mode |
(char) Path to local cached file or initial download is required
getAnnotationFiles(verbose = TRUE, vignette= TRUE)getAnnotationFiles(verbose = TRUE, vignette= TRUE)
This function controls the 'shiny.launch.browser' option to launch uncoverapp in an external 'browser', the RStudio viewer '"viewer"', or a new '"window"' in RStudio.
run.uncoverapp(where = c("browser", "viewer", "window"))run.uncoverapp(where = c("browser", "viewer", "window"))
where |
accept '"browser'" , '"viewer'" or '"window'". The option sets where uncoverapp will be launched. Using NULL, uncoverapp will use default After running 'run.uncoverapp(where="window")' the shiny app appears in your chosen location. |
This return a Shiny App. The is no value
## Only run this example in interactive R sessions if (interactive()) { run.uncoverapp(where="window") }## Only run this example in interactive R sessions if (interactive()) { run.uncoverapp(where="window") }
This function launches unCOVERApp, a
Shiny application for clinical assessment of sequence coverage.
Setting where uncoverapp will be launched with following where option:
'"browser'" in user default browser, '"viewer'" RStudio viewer and '"window'"
in a new Rstudio window.
uncoverAPP()uncoverAPP()
This return a Shiny App. The is no value
Emanuela Iovino
## Not run: file.name='../path/sorted.bed.gz' tbi='.../path/sorted.bed.gz.tbi' app() ## End(Not run) ## Only run this example in interactive R sessions if (interactive()) { app() }## Not run: file.name='../path/sorted.bed.gz' tbi='.../path/sorted.bed.gz.tbi' app() ## End(Not run) ## Only run this example in interactive R sessions if (interactive()) { app() }
a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.
Maintainer: Emanuela Iovino [email protected]
Authors:
Tommaso Pippucci [email protected]
Useful links:
Report bugs at https://github.com/Manuelaio/uncoverappLib/issues