In federicomarini/annoFuseData: Data Package for the annoFuse Bioconductor Package

Compiled date: r Sys.Date()

Last edited: 2020-11-11

License: r packageDescription("annoFuseData")[["License"]]

knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  error    = FALSE,
  warning  = FALSE,
  eval     = TRUE,
  message  = FALSE,
  fig.width = 10
)
options(width = 100)

Datasets for `annoFuse`

library("annoFuseData")

Example output files from fusion callers {-}

arriba_example.tsv
starfusion_example.tsv

ff_arriba <- read.delim(system.file("extdata", "arriba_example.tsv", package = "annoFuseData"))
ff_starfusion <- read.delim(system.file("extdata", "starfusion_example.tsv", package = "annoFuseData"))
head(ff_arriba)
head(ff_starfusion)

These files are e.g. used in the annoFuse_single_sample() function.

Expression data {-}

example.rsem.genes.results.gz

expression_tbl <- read.delim(system.file("extdata", "example.rsem.genes.results.gz", package = "annoFuseData"))
head(expression_tbl)

Examples of output files from the `annoFuse` workflow {-}

FilteredFusionAnnoFuse.tsv
PutativeDriverAnnoFuse.tsv

out_annofuse_putative <- read.delim(
  system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData"))
out_annofuse_filtered <- read.delim(
  system.file("extdata", "FilteredFusionAnnoFuse.tsv", package = "annoFuseData"))

head(out_annofuse_putative)
head(out_annofuse_filtered)

Adding domain level information and exon information {-}

Will describe and give some initial overview on each dataset:

pfamDataBioMart.RDS
exonsToPlot.RDS

data_pfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
head(data_pfam)
data_exons <- readRDS(system.file("extdata", "exonsToPlot.RDS", package = "annoFuseData"))
head(data_exons)
dim(data_exons)

Analysis of TCGA data {-}

merged_arriba_tcga.tsv
merged_starfusion_tcga.tsv
sample_aliquot_tcga.tsv
final_fusion_mmc2.txt

tcga_arriba_df <- read.delim(system.file("extdata", "merged_arriba_tcga.tsv", package = "annoFuseData"))
tcga_starfusion_df <- read.delim(system.file("extdata", "merged_starfusion_tcga.tsv", package = "annoFuseData"))

head(tcga_arriba_df)
head(tcga_starfusion_df)

tcga_manifest <- read.delim(system.file("extdata", "sample_aliquot_tcga.tsv", package = "annoFuseData"))
final_fusion <- read.delim(system.file("extdata", "final_fusion_mmc2.txt", package = "annoFuseData"))

head(tcga_manifest)
head(final_fusion)

Scoring the annotated fusion calls {-}

zscored_annotation

expr_collapsed.rds
gtex_collapsed.rds

expressionMatrix <- readRDS(system.file("extdata", "expr_collapsed.rds", package = "annoFuseData"))
gtex_collapsed <- readRDS(system.file("extdata", "gtex_collapsed.rds", package = "annoFuseData"))

head(expressionMatrix)
head(gtex_collapsed)

Reference tables for gene lists and fusions {-}

fusion_driver

genelistreference.txt
fusionreference.txt

geneListReferenceDataTab <- read.delim(
  system.file("extdata", "genelistreference.txt", package = "annoFuseData"), 
  stringsAsFactors = FALSE)
fusionReferenceDataTab <- read.delim(
  system.file("extdata", "fusionreference.txt", package = "annoFuseData"), 
  stringsAsFactors = FALSE)
head(geneListReferenceDataTab)
head(fusionReferenceDataTab)