call_TCs: Call TSS or PAS sites as clusters of reads from 5'- or 3'-tag...

In Maxim-Ivanov/TranscriptomeReconstructoR: Data-driven Annotation of the Transcriptome

Call TSS or PAS sites as clusters of reads from 5'- or 3'-tag sequencing data

Description

Call TSS or PAS sites as clusters of reads from 5'- or 3'-tag sequencing data

Usage

call_TCs(
  data,
  min_support = length(data),
  min_tpm = 0.05,
  max_gap = 50,
  q_trim = 0.05,
  min_score = 0.25
)

Arguments

data	GRangesList object with all elements having the "score" mcols.
min_support	Integer >= 1 (but not exceeding the number of replicates in data)
min_tpm	Non-negative numeric.
max_gap	Non-negative integer.
q_trim	Numeric in the range (0, 1), or NULL.
min_score	Non-negative numeric.

Value

GRanges object containing coordinates of called tag clusters.

Details

The input data is returned by the load_BAM_files() function.
Only genomic positions with non-zero signal in at least min_support replicates are considered for TSS/PAS calling.
After merging the replicates, only genomic positions with at least min_tpm signal are considered as positions with valid signal.
Genomic positions with valid signal separated by not more than max_gap bases are merged into tag cluster (TC) candidates.
TC candidates are trimmed to retain only genomic positions containing 1 - q_trim fraction of the signal.
Only TCs with TPM (averaged among replicates) exceeding min_score are considered valid TSS/PAS.

Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Oct. 3, 2023, 11:19 p.m.