maaper {MAAPER}

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 pas_annotation files for ID formats.

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, [e-mail]

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)