PsiteMapping: P-site mapping

In jipingw/RiboDiPA: Differential pattern analysis for Ribo-seq data

P-site mapping

Description

This function computes the corresponding P-site locations of all RPFs and the total RPF read counts for all genes and samples.

Usage

psiteMapping(bam_file_list, gtf_file, psite.mapping = "auto", 
    cores = NULL)

Arguments

bam_file_list	A vector of bam file names to be tested. Users should include path names if not located in the current working directory. Index files (.bai) will be generated if not already present.
gtf_file	Annotation file used to generate the BAM alignments. Note that a GTF file sourced from one organization (e.g. Ensembl) cannot be used with BAM files aligned with a GTF file sourced from another organization (e.g. UCSC).
psite.mapping	Rules for P-site offsets, to map a given read length of RPF to a P-site. Input for this parameter is a string input, or a user defined matrix assigning the P-site mapping rules. Strings include: "center" for taking center of the read as the P-site, and "auto" for an optimal P-site offset, which is the default. A user defined matrix should include two columns: "qwidth" and "psite", where "qwidth" is the range of possible read lengths and "psite" is the corresponding offset from the 5' end to map to the P-site.
cores	The number of cores to use for parallel execution. If not specified, the number of cores is set to the value of detectCores(logical = FALSE).

Details

All exons from the same gene are concatenated into a total transcript in order to get a merged picture of translation, using the reduce() function from the GRanges package to accomplish the concatenation. Then, RPFs are mapped with respect to the total transcript and the P-site positions are inferred accordingly.

If 'psite.mapping' is unspecified, a two-step algorithm on start codons of CDS regions is used to compute optimal P-site offsets, following Lauria et al (2018). First, for a given read length, the offset is calculated by taking the distance between the first nucleotide of the start codon and the 5' most nucleotide of the read, and then defining the offset as the 5' position with the most reads mapped to it. This process is repeated for all read lengths and then the temporary global offset is defined to be the offset of the read length with the maximum count. Lastly, for each read length, the adjusted offset is defined to be the one corresponding to the local maximum found in the profiles of the start codons closest to the temporary global offset.

The function will return a list of matrices that can then be used for data binning and downstream analysis, among other data objects.

Value

coverage	A list object of matrices. Each element is a matrix representing the P-site footprints of a gene. Rows correspond to replicates and columns corrspond to nucleotide location with respect to the total transcript. Each column is named by its genomic coordinate.
counts	A matrix object of read counts. Rows correspond to genes and columns correspond to replicates.
psite.mapping	The P-site (or A-site) mapping rule used to map RPFs to P-site positions.
exons	A List object of matrices. Each element contains the relative start and end positions of exons in the gene with respect to the total transcript for that given gene, as well as genomic start and end coordinates.

References

Lauria, F., Tebaldi, T., Bernabò, P., Groen, E., Gillingwater, T. H., & Viero, G. (2018). riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. PLoS computational biology, 14(8), e1006169.

Examples

library(BiocFileCache)
file_names <- c("WT1.bam", "WT2.bam", "MUT1.bam", "MUT2.bam", "eg.gtf")
url <- "https://github.com/jipingw/RiboDiPA-data/raw/master/"
bfc <- BiocFileCache()
bam_path <- bfcrpath(bfc,paste0(url,file_names))

classlabel <- data.frame(
    condition = c("mutant", "mutant", "wildtype", "wildtype"),
    comparison = c(2, 2, 1, 1)
)
rownames(classlabel) <- c("mutant1","mutant2","wildtype1","wildtype2") 

data.psite <- psiteMapping(bam_file_list = bam_path[1:4], 
    gtf_file = bam_path[5], psite.mapping = "auto", cores = 2)

jipingw/RiboDiPA documentation built on Dec. 10, 2024, 8:46 p.m.