tallies
Tally VRanges
Bundled with VariantToolsData · exported, loads via data()
Class
–
Missing
–
Format
rda · xz
version 3 · 1.4 MB
File
data/tallies.rda
Fingerprint
–
Format documented
Yes
Source
Computed from the alignments of the FASTQ files found in the `inst/extdata` directory. Repeat regions (see repeats) were excluded. For example, for one replicate, library(gmapR) extdata.dir <- system.file("extdata", package="VariantToolsData") bams <- BamFileList(tools::list_files_with_exts(extdata.dir, "bam")) data(repeats, package = "VariantToolsData") param <- TallyVariantsParam(TP53Genome(), mask = repeats, read_pos=TRUE, read_length=75L) tallies <- split(tallyVariants(bams, param), ~ sampleNames) This assumes that the BAM files have been generated for the current version of the TP53 genome: param <- GsnapParam(TP53Genome(), unique_only = TRUE, molecule = "DNA") first.fastq <- dir(extdata.dir, "first.fastq", full.names=TRUE) last.fastq <- dir(extdata.dir, "last.fastq", full.names=TRUE) output <- gsnap(first.fastq, last.fastq, param) bams <- as(output, "BamFileList")
Columns
Nothing inside this object was measured, so there is no column list, no counts and no fingerprint to compare it with. An S4 assay container whose dimensions sit behind accessor functions this reader does not call. What is recorded is the file it lives in and which releases carry it.
Version history
| Version | Released | Size | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.22 | 2025-10-29 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.21 | 2025-04-15 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.20 | 2024-10-29 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.19 | 2024-04-30 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.18 | 2023-10-24 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.17 | 2023-04-25 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.16 | 2022-11-01 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.15 | 2022-04-26 | – | Not compared | rda · xz version 3 · 1.4 MB | degraded |
| 3.14 | 2021-10-26 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.13 | 2021-05-19 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.12 | 2020-10-27 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.11 | 2020-04-27 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.10 | 2019-10-29 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.9 | 2019-05-02 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.8 | 2018-10-30 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.7 | 2018-04-30 | – | Not compared | rda · gzip version 2 · 2.2 MB | degraded |
| 3.6 | 2017-10-30 | – | Not compared | rda · xz version 2 · 1.3 MB | degraded |
| 3.5 | 2017-08-16 | – | – | rda · xz version 2 · 1.3 MB | degraded |