analyzeFeatures: Analysis of splice graph features from BAM files

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

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)

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