runMain: _ workflow: Test transcripts for NMD feature

In fursham-h/ponder:

Description

THIS FUNCTION IS PART OF THE _ PROGRAM WORKFLOW. This function will analyze the assembled transcripts for NMD features

Usage

runMain(
  report_df,
  inputExonsbyTx,
  basicExonsbyCDS,
  basicExonsbyTx,
  genome,
  testforNMD = TRUE,
  PTC_dist = 50,
  testNonClassicalNMD = FALSE,
  testforAS = FALSE
)

Arguments

report_df	dataframe of a list of assembled transcripts. It is recommended to create this object using prepareAnalysis function from the workflow. see ?prepareAnalysis
inputExonsbyTx	GRangesList of exon coordinates of assembled transcripts grouped by transcript name. It is recommended to create this object using prepareAnalysis function from the workflow. see ?prepareAnalysis
basicExonsbyCDS	GRangesList of exon coordinates of reference CDS grouped by transcript name. It is recommended to create this object using prepareAnalysis function from the workflow. see ?prepareAnalysis
genome	DNAstring containing genome sequence
PTC_dist	Numerical value referring to minimium distance of premature stop codon to last exon junction
testNonClassicalNMD	Boolean value (TRUE/FALSE) on whether to test for non-classical NMD features
basicTX_df	dataframe of a list of reference CDS transcripts. It is recommended to create this object using prepareAnalysis function from the workflow. see ?prepareAnalysis

Value

updated form of report_df

fursham-h/ponder documentation built on Dec. 27, 2019, 12:15 a.m.