SGSeq (version 1.6.5)

analyzeFeatures: 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

Value

SGFeatureCounts object

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.

Examples

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