annoFuse_single_sample: Single Sample use for annoFuse

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

Single Sample use for annoFuse

Description

Performs artifact filter to remove readthroughs,red flags and performs expression filtering with user provided expression Matrix and expression threshold

Usage

annoFuse_single_sample(
  fusionfileArriba,
  fusionfileStarFusion,
  expressionFile = NULL,
  expressionFilter = 1,
  tumorID = "tumorID",
  readingFrameFilter = "in-frame|frameshift|other",
  readthroughFilter = FALSE,
  artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG",
  junctionReadCountFilter = 1,
  spanningFragCountFilter = 10
)

Arguments

fusionfileArriba	A dataframe from arriba fusion caller
fusionfileStarFusion	A dataframe from starfusion caller
expressionFile	Expression matrix for samples used in cohort for fusion calls
expressionFilter	FPKM/TPM threshold for not expressed
tumorID	Sample name to be used
readingFrameFilter	A regex to capture readingframe (eg. in-frame|frameshift|other)
readthroughFilter	Boolean for filtering readthroughs
artifactFilter	A red flag filter from Annotation ; in OpenPBTA annotation is from FusionAnnotator column "annots"
junctionReadCountFilter	An integer threshold for JunctionReadCount
spanningFragCountFilter	An integer threshold for (SpanningFragCount - JunctionReadCount)

Value

Standardized fusion calls annotated with gene list and fusion list provided in reference folder

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
)

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