zscored_annotation: Annotates standardizes fusion calls calls with zscored...

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Annotates standardizes fusion calls calls with zscored expression value from either GTEx/cohort

Description

The input should have the following standardized columns to run through this GTEx/cohort normalization function "Sample" Unique SampleIDs used in your RNAseq dataset "FusionName" GeneA–GeneB ,or if fusion is intergenic then Gene1A/Gene2A–GeneB

Usage

zscored_annotation(
  standardFusioncalls,
  zscoreFilter,
  saveZscoredMatrix,
  normData,
  expressionMatrix
)

Arguments

standardFusioncalls	Annotates standardizes fusion calls from callers STARfusion| Arriba or QC filtered fusion
zscoreFilter	Zscore value to use as threshold for annotation of differential expression
saveZscoredMatrix	File to save zscored matrix calculated for the normalized data and expression matrix
normData	normalizing expression dataset to calculate zscore
expressionMatrix	Expression matrix associated with the fusion calls

Value

expression_annotated_fusions is a standardized fusion call set with standard

Examples

standardFusioncalls <- annoFuse::annoFuse_single_sample(
  # Example files are provided in extdata, at-least 1 fusionfile is required along
  # with its rsem expression file
  fusionfileArriba = system.file("extdata", "arriba_example.tsv", package = "annoFuseData"),
  fusionfileStarFusion = system.file("extdata", "starfusion_example.tsv", package = "annoFuseData"),
  expressionFile = system.file(
    "extdata", "example.rsem.genes.results.gz",
    package = "annoFuseData"
  ),
  tumorID = "BS_W97QQYKQ",
  # multiple read flag values for filtering using FusionAnnotator values
  artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG",
  # keep all in-frame , frameshift and other types of Fusion_Type
  readingFrameFilter = "in-frame|frameshift|other",
  # keep all fusions with atleast 1 junction read support
  junctionReadCountFilter = 1,
  # keep only fusions where spanningFragCount-junctionReadCountFilter less than equal to 10
  spanningFragCountFilter = 10,
  # keep read throughs
  readthroughFilter = FALSE
)
expressionMatrix <- readRDS(system.file("extdata", "expr_collapsed.rds", package = "annoFuseData"))
normData <- readRDS(system.file("extdata", "gtex_collapsed.rds", package = "annoFuseData"))
zscoredStandardFusioncalls <- zscored_annotation(standardFusioncalls,
  zscoreFilter = 2,
  normData = normData,
  expressionMatrix = expressionMatrix
)

d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.