annoFuse_single_sample: Single Sample use for annoFuse

Description Usage Arguments Value Examples

View source: R/annoFuse_single_sample.R

Description

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

Usage

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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

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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 March 11, 2021, 9:05 p.m.