predictTxFeatures {SGSeq} | R Documentation

## Splice junction and exon prediction from BAM files

### Description

Splice junctions and exons are predicted for each sample and merged across samples. Terminal exons are filtered and trimmed, if applicable. For details, see the help pages for `predictTxFeaturesPerSample`, `mergeTxFeatures`, and `processTerminalExons`.

### Usage

    predictTxFeatures(sample_info, which = NULL, alpha = 2, psi = 0,
      beta = 0.2, gamma = 0.2, min_junction_count = NULL, min_anchor = 1,
      max_complexity = 20, min_n_sample = 1, min_overhang = NA,
      verbose = FALSE, cores = 1)

### Arguments

`sample_info` | Data frame with sample information. Required columns are “sample_name”, “file_bam”, “paired_end”, “read_length”, “frag_length” and “lib_size”. Library information can be obtained with function `getBamInfo`.
`which` | `GRanges` of genomic regions to be considered for feature prediction, passed to `ScanBamParam`
`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
`min_junction_count` | Minimum fragment count required for a splice junction to be included. If specified, argument `alpha` is ignored.
`min_anchor` | Integer specifiying minimum anchor length
`max_complexity` | Maximum allowed complexity. If a locus exceeds this threshold, it is skipped, resulting in a warning. Complexity is defined as the maximum number of unique predicted splice junctions overlapping a given position. High complexity regions are often due to spurious read alignments and can slow down processing. To disable this filter, set to `NA`.
`min_n_sample` | Minimum number of samples a feature must be observed in to be included
`min_overhang` | Minimum overhang required to suppress filtering or trimming of predicted terminal exons (see the manual page for `processTerminalExons`). Use `NULL` to disable processing (disabling processing is useful if results are subsequently merged with other predictions and processing is postponed until after the merging step).
`verbose` | If `TRUE`, generate messages indicating progress
`cores` | Number of cores available for parallel processing

### Value

`TxFeatures` object

### Author(s)

Leonard Goldstein

### Examples

    path <- system.file("extdata", package = "SGSeq")
    si$file_bam <- file.path(path, "bams", si$file_bam)
    txf <- predictTxFeatures(si, gr)

[Package SGSeq version 1.20.0 Index]