filterFeatures: Filter predicted features
In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description Usage Arguments Details Value Author(s)

Filter previously predicted features using more stringent criteria.

1 2	filterFeatures(features, paired_end, read_length, frag_length, lib_size, min_junction_count = NULL, alpha, psi, beta, gamma)

`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

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”.

TxFeatures object with filtered features

Leonard Goldstein

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.