data-raw/sod1_junctions.R

In dzhang32/ggtranscript: Visualizing Transcript Structure and Annotation using 'ggplot2'

# Load libraries ----------------------------------------------------------

library(tidyverse)
library(snapcount)
library(SummarizedExperiment)

# Main --------------------------------------------------------------------

# obtain gtex junctions across SOD1
sod1_query <- snapcount::QueryBuilder(compilation = "gtex", regions = "SOD1")

# keeping only unannotated junctions
# from liver where SOD1 is highly expressed
# https://gtexportal.org/home/gene/SOD1
sod1_query <- set_row_filters(sod1_query, annotated == 0)
sod1_query <- set_column_filters(sod1_query, SMTS == "Liver")

sod1_junctions <- snapcount::query_jx(sod1_query)

# obtain mean counts
mean_counts <-
    sod1_junctions %>%
    SummarizedExperiment::assays() %>%
    .[["counts"]] %>%
    as.matrix() %>%
    rowMeans()

sod1_junctions <- sod1_junctions %>%
    SummarizedExperiment::rowRanges() %>%
    as.data.frame() %>%
    dplyr::as_tibble()

# minor QC and tidying of the junctions
sod1_junctions <-
    sod1_junctions %>%
    dplyr::mutate(mean_count = mean_counts) %>%
    dplyr::filter(mean_count > 0.3) %>%
    dplyr::select(
        seqnames,
        start,
        end,
        strand,
        mean_count
    )

# Save data ---------------------------------------------------------------

usethis::use_data(
    sod1_junctions,
    compress = "gzip",
    overwrite = TRUE
)