stupornova33 / misipi.rna Goto Github PK

For more details about the package or to cite, please visit https://www.biorxiv.org/content/10.1101/2023.05.07.539760v1.

Characterization of small RNA pathways

In order to install MiSiPi.RNA, you must first install devtools and BiocManager:

install.packages("devtools")

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  
devtools::install_github("stupornova33/MiSiPi.RNA")

library(MiSiPi.RNA)

In order for this package to work, you must also have RNAfold from the ViennaRNA package installed. You will need the path to the RNAfold executable. See https://www.tbi.univie.ac.at/RNA/ for installation.

The input for any of MiSiPi.RNA's main functions is an object created by the set_vars() function. Running set_vars will always be the first step in using this package. Below is a description of each of the parameters that will be passed to set_vars(). These should be changed based on your needs.

• roi - A bed file listing your regions of interest
• bam_file - A BAM file of aligned reads. Index file must also be present
• genome - A genome fasta file. Chromosome names must match the bed file
• min_read_count - This filters out loci with low mapping reads. Defaults to 1
• plot_output - (TRUE or FALSE) If TRUE, MiSiPi.RNA will output plots as pdfs
• path_to_RNAfold - Full path to RNAfold executable
• pi_pal - Palette option for the generated piRNA heatmap (see below)
• si_pal - Palette option for the generated siRNA heatmap (see below)
• annotate_region - (TRUE or FALSE) Plots annotated gene features below the hairpin arc plot which is useful for characterizing cisNAT loci
• weight_reads - Determines if read counts will be weighted. ("Top", "locus_norm", or "None")
• gtf_file - Full path to a 9 column GTF file. Required only if annotate_region is TRUE
• write_fastas - (TRUE or FALSE) If TRUE, MiSiPi.RNA will write read pairs from functions to a file. Default is FALSE
• out_type - ("pdf" or "png") Specifies the output type. Default is "pdf"

vars <- set_vars(roi = "path/to/bed",
                bam_file = "path/to/bam", 
                genome = "path/to/genome",
                min_read_count = 1,
                plot_output = TRUE, 
                path_to_RNAfold = "path/to/ViennaRNA/RNAfold.exe",
                pi_pal = "BlYel",
                si_pal = "RdYlBl",
                annotate_region = TRUE,
                weight_reads = "None",
                gtf_file = "path/to/gtf",
                write_fastas = FALSE,
                out_type = "pdf")

Palette options are:

• "RdYlBl"
• "BlYel"
• "yelOrRed"
• "MagYel"
• "Greens"

miRNA_function(vars)


piRNA_function(vars)


siRNA_function(vars)

# To run the above functions all at once
misipi_rna(vars)