getAltTSS {MOCHA}

Annotate Peaks falling in Transcription Start Sites (TSS) and identify alternatively regulated TSSs for each gene.

Description

getAltTSS Pulls out all peaks that fall in TSS, annotates them with the name of gene, and identifies genes that have evidence for alternatively regulated TSSs, including both type i (only some of the open TSSs for a gene are significantly more (or less) accessible), and type ii (multiple TSSs are significant different, with some being more accessible and others less). Alternatively, this function will return all open TSSs with differential measurements if the returnAllTSS flag is set to TRUE.

Usage

getAltTSS(
  completeDAPs,
  returnAllTSS = FALSE,
  nuancedTSS = TRUE,
  nuancedTSSGap = 150,
  threshold = 0.2,
  TxDb,
  OrgDb
)

Arguments

completeDAPs

GRanges object that contains the differential measurements across all peaks (unfiltered DAPs). Will also work with data.frame or data.table version of a GRanges object. If you want alternatively regulated TSSs, the object must include a column names 'FDR', and 'Log2FC_C', which is standard for MOCHA differentials.

returnAllTSS

Flag to return all TSSs with DAPs measurements, without filtering for alternative TSS usage. If multiple TSSs fall within the same tile, then that tile will be repeated for each TSS.

nuancedTSS

True/False flag to determine if alternative TSS genes should be filtered out if all their differential TSS usage falls within too small of a range. Default is TRUE

nuancedTSSGap

Minimum distance betweeen TSSs needed for them to considered distinctly regulated TSSs. If two TSSs are too close, it is unclear and highly unlikely that ATAC data can distinguish between them. Default is 150 bp.

threshold

FDR Threshold for determining significant vs non-significant changes in accessibility. Following MOCHA's standards, default is 0.2.

TxDb

The TxDb-class transcript annotation package for your organism (e.g. "TxDb.Hsapiens.UCSC.hg38.refGene"). This must be installed. See Bioconductor AnnotationData Packages.

OrgDb

The OrgDb-class genome wide annotation package for your organism (e.g. "org.Hs.eg.db"). This must be installed. See Bioconductor AnnotationData Packages

Value

tpeaks A GRanges containing annotated peaks falling in TSS