| Title: | Reads from Two Lung Cancer Cell Lines |
|---|---|
| Description: | Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. |
| Authors: | Cory Barr, Michael Lawrence |
| Maintainer: | Michael Lawrence <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 0.50.0 |
| Built: | 2026-10-10 11:03:51 UTC |
| Source: | https://github.com/bioc/LungCancerLines |
This package was created to use in examples and test sets for the gmapR and VariationTools packages.
| Package: | TP53Genome |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2012-09-05 |
| License: | Artistic-2.0 |
By calling data(p53Genome), users will have access to a GmapGenome object for the TP53 genome.
Cory Barr
Maintainer: Cory Barr <[email protected]>
data(p53Genome)data(p53Genome)
Gets a BamFileList pointing to BAM files containing read
alignments for the H1993 and H2073 RNA-seq samples. The files are
the “analyzed” BAM files as output by the HTSeqGenie
package.
LungCancerBamFiles()LungCancerBamFiles()
The reads were aligned to genome TP53Genome,
using the following parameters:
splicing: knownGene
novelsplicing: 1
indel_penalty: 1
distant_splice_penalty: 1
suboptimal_levels: 2
npaths: 10
Note that the BAM files contain only unique alignments.
A BamFileList pointing to two BAM files, one for H1993, one for
H2073.
Michael Lawrence
LungCancerBamFiles()LungCancerBamFiles()
Returns a character vector of file paths to the demo Fastq files.
LungCancerFastqFiles()LungCancerFastqFiles()
A character vector, named according to “H[1993/2073].[first/last]”.
Michael Lawrence
LungCancerFastqFiles()LungCancerFastqFiles()