| Title: | Analysis of Alternative Polyadenylation Using 3' End-Linked Reads |
| Version: | 1.1.1 |
| Description: | A computational method developed for model-based analysis of alternative polyadenylation (APA) using 3' end-linked reads. It accurately assigns 3' RNA-seq reads to polyA sites through statistical modeling, and generates multiple statistics for APA analysis. Please also see Li WV, Zheng D, Wang R, Tian B (2021) <doi:10.1186/s13059-021-02429-5>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.1 |
| Imports: | parallel, GenomicRanges, GenomicAlignments, GenomicFeatures, GenomeInfoDb, stats, utils, Rsamtools, IRanges, MASS |
| URL: | https://github.com/Vivianstats/MAAPER, https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02429-5 |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2021-08-14 00:15:35 UTC; wei |
| Author: | Wei Vivian Li 
[aut, cre] |
| Maintainer: | Wei Vivian Li <vivian.li@rutgers.edu> |
| Repository: | CRAN |
| Date/Publication: | 2021-08-14 14:20:05 UTC |
Model-based analysis of alternative polyadenylation using 3’ end-linked reads
Description
Model-based analysis of alternative polyadenylation using 3’ end-linked reads
Usage
maaper(
gtf,
pas_annotation,
output_dir,
bam_c1,
bam_c2,
read_len,
ncores = 1,
num_pas_thre = 25,
frac_pas_thre = 0.05,
dist_thre = 600,
num_thre = 50,
run = "all",
subset = NULL,
region = "all",
gtf_rds = NULL,
verbose = FALSE,
paired = FALSE,
bed = FALSE
)
Arguments
gtf |
A character specifying the full path of the GTF file (reference genome); |
pas_annotation |
A list containing the pas annotation. MAAPER provides processed annotation information from PolyA_DB v3 on its Github page. |
output_dir |
A character specifying the full path of the output directory, which is used to store all intermdediate and final outputs. |
bam_c1 |
A character vector specifying the full paths to the bam files for condition 1 (control). The length of the vector equals the number of samples. |
bam_c2 |
A character vector specifying the full paths to the bam files for condition 2 (experiment). The length of the vector equals the number of samples. |
read_len |
An integer specifying the read length. |
ncores |
An integer specifying the number of cores used in parallel computation. |
num_pas_thre |
An integer specifying the threhold on PAS's read number. Defaults to 25. |
frac_pas_thre |
A numeric specifying the threshold on PAS's fraction. Defaults to 0.05. |
dist_thre |
An integer specifying the threshold on fragment length. Defaults to 600. |
num_thre |
An integer specifying the threhold on gene's read number. Defaults to 50. |
run |
"all" (default) or "skip-train". For test and debug only. |
subset |
A character vector specifying genes' Ensembl IDs if only a subset of genes need to be analyzed.
Check the |
region |
"all" (default). For test and debug only. |
gtf_rds |
NULL (default). For test and debug only. |
verbose |
FALSE (default). For test and debug only. |
paired |
A boolean indicating whether to perform paired test instead of unpaired test (defaults to FALSE). |
bed |
Aboolean indicating whether bedGraph files should be output for visualization in genome browser. |
Value
maaper saves two text files, gene.txt and pas.txt, to out_dir.
pas.txt contains the gene names, predicted PASs, and their corresponding fractions in the two conditions.
gene.txt contains the genes' PAS number, p values, RED, RLDu, and RLDi scores.
Author(s)
Wei Vivian Li, vivian.li@rutgers.edu
Examples
## Not run:
# data used in this example can be found on the package's Github page
pas_annotation = readRDS("./mouse.PAS.mm9.rds")
gtf = "./gencode.mm9.chr19.gtf"
bam_c1 = "./NT_chr19_example.bam"
bam_c2 = "./AS_4h_chr19_example.bam"
maaper(gtf, pas_annotation, output_dir = "./",
bam_c1, bam_c2, read_len = 76, ncores = 1)
## End(Not run)