analyzeFeatures {SGSeq} | R Documentation

## Analysis of splice graph features from BAM files

### Description

High-level function for the prediction and quantification of splice junctions, exon bins and splice sites from BAM files.

### Usage

    analyzeFeatures(sample_info, which = NULL, features = NULL,
      predict = is.null(features), alpha = 2, psi = 0, beta = 0.2,
      gamma = 0.2, min_junction_count = NULL, min_anchor = 1,
      min_n_sample = 1, min_overhang = NA, annotation = NULL,
      max_complexity = 20, 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`
`features` | `TxFeatures` or `SGFeatures` object
`predict` | Logical indicating whether transcript features should be predicted from BAM files
`alpha` | Minimum FPKM required for a splice junction to be included
`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
`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).
`annotation` | `TxFeatures` object used for annotation
`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`.
`verbose` | If `TRUE`, generate messages indicating progress
`cores` | Number of cores available for parallel processing

### Details

Splice junctions and exons are predicted from BAM files with `predictTxFeatures`.

Known features can be provided as `TxFeatures` or `SGFeatures` via argument `features`.

If `features` is not `NULL` and `predict` is `TRUE`, known features are augmented with predictions.

Known and/or predicted transcript features are converted to splice graph features. For details, see `convertToSGFeatures`.

Optionally, splice graph features can be annotated with respect to a `TxFeatures` object provided via argument `annotation`. For details, see the help page for function `annotate`.

Finally, compatible fragment counts for splice graph features are obtained from BAM files with `getSGFeatureCounts`.

### Value

`SGFeatureCounts` object

### Author(s)

Leonard Goldstein

### Examples

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

[Package SGSeq version 1.18.0 Index]