filterFeatures: Filter predicted features

Description Usage Arguments Details Value Author(s)

View source: R/features-filter.R

Description

Filter previously predicted features using more stringent criteria.

Usage

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filterFeatures(features, paired_end, read_length, frag_length, lib_size,
  min_junction_count = NULL, alpha, psi, beta, gamma)

Arguments

features

TxFeatures object with predicted features, including metadata columns “N”, “N_splicesite” and “coverage”.

paired_end

Logical, TRUE for paired-end data, FALSE for single-end data

read_length

Read length required for use with alpha

frag_length

Fragment length for paired-end data required for use with alpha

lib_size

Number of aligned fragments required for use with alpha

min_junction_count

Minimum fragment count required for a splice junction to be included. If specified, argument alpha is ignored.

alpha

Minimum FPKM required for a splice junction to be included. Internally, FPKMs are converted to counts, requiring arguments read_length, frag_length and lib_size. alpha is ignored if argument min_junction_count is specified.

psi

Minimum splice frequency required for a splice junction to be included

beta

Minimum relative coverage required for an internal exon to be included

gamma

Minimum relative coverage required for a terminal exon to be included

Details

Initial predictions with predictTxFeatures must have been performed with include_counts = TRUE and retain_coverage = TRUE, so that predicted features contain metadata columns “N”, “N_splicesite” and “coverage”.

Value

TxFeatures object with filtered features

Author(s)

Leonard Goldstein


ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.