predictTxFeatures: Splice junction and exon prediction from BAM files

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

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)

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