bambu {bambu} | R Documentation |
This function takes bam file of genomic alignments and performs isoform recontruction and gene and transcript expression quantification. It also allows saving of read class files of alignments, extending provided annotations, and quantification based on extended annotations. When multiple samples are provided, extended annotations will be combined across samples to allow comparison.
bambu( reads = NULL, rcFile = NULL, rcOutDir = NULL, annotations = NULL, genome = NULL, stranded = FALSE, ncore = 1, yieldSize = NULL, opt.discovery = NULL, opt.em = NULL, discovery = TRUE, quant = TRUE, verbose = FALSE, lowMemory = FALSE )
reads |
A string or a vector of strings specifying the paths of bam
files for genomic alignments, or a |
rcFile |
A string or a vector of strings specifying the read
class files that are saved during previous run of |
rcOutDir |
A string variable specifying the path to where read class files will be saved. |
annotations |
A |
genome |
A fasta file or a BSGenome object. |
stranded |
A boolean for strandedness, defaults to FALSE. |
ncore |
specifying number of cores used when parallel processing is used, defaults to 1. |
yieldSize |
see |
opt.discovery |
A list of controlling parameters for isoform reconstruction process:
|
opt.em |
A list of controlling parameters for quantification algorithm estimation process:
|
discovery |
A logical variable indicating whether annotations are to be extended for quantification. |
quant |
A logical variable indicating whether quantification will be performed |
verbose |
A logical variable indicating whether processing messages will be printed. |
lowMemory |
Read classes will be processed by chromosomes when lowMemory is specified. This option provides an efficient way to process big samples. |
Main function
bambu
will output different results depending on whether
quant mode is on. By default, quant is set to TRUE, so
bambu
will generate a SummarizedExperiment object that contains
the transcript expression estimates. Transcript expression estimates can be
accessed by counts(), including the following variables
expression estimates
sequencing depth normalized estimates
estimates of read counts mapped as full length reads for each transcript
estimates of read counts mapped as partial length reads for each transcript
counts of reads that are uniquely mapped to each transcript
raw estimates
Output annotations that are usually the annotations with/without novel transcripts/genes added, depending on whether discovery mode is on can be accessed by rowRanges() Transcript to gene map can be accessed by rowData(), with eqClass that defining equivalent class for each transcript
In the case when quant is set to FALSE, i.e., only transcript
discovery is performed, bambu
will report the grangeslist of
the extended annotations.
## ===================== test.bam <- system.file("extdata", "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam", package = "bambu") fa.file <- system.file("extdata", "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa", package = "bambu") gr <- readRDS(system.file("extdata", "annotationGranges_txdbGrch38_91_chr9_1_1000000.rds", package = "bambu")) se <- bambu(reads = test.bam, annotations = gr, genome = fa.file, discovery = TRUE, quant = TRUE)