In dongzhuoer/rexseek: Matrix Processing in the exSeek Project

knitr::opts_chunk$set(echo = F, error = T)

library(tidyverse)

mat_raw <- 'data-raw/external/scirep_sequential_qc.txt' %>% rexseek::read_mat()
sample_class <- 'data-raw/external/scirep_classes.txt' %>% readr::read_csv(T, 'cc')

orignial matrix

mat_raw[1:10, 1:6]

filter low-expressed genes

mat <- mat_raw %>% rexseek::filter_low()

mat[1:10, 1:6]

Show highest expressed genes

rexseek::as_SingleCellExperiment(mat, col_data = sample_class) %>%
    rexseek::plot_highest_exprs()

normalization

headers <- paste0(
    c('before', 'TMM', 'RLE', 'CPM', 'CPM top_n', 'CPM remove certain RNA type', 'CPM reference gene'), 
    ' normalization'
)
mat_norms <- list(
    mat,
    rexseek::norm_tmm(mat), 
    rexseek::norm_rle(mat), 
    rexseek::norm_cpm(mat), 
    rexseek::norm_cpm_top(mat, 20), 
    rexseek::norm_cpm_rm(mat, c('miRNA', 'piRNA')), 
    rexseek::norm_cpm_refer(mat, rexseek::suggest_refer$id)
)

report_mat <- function(...) {
    child_output <- knitr::knit_child(
        system.file('rmd/norm_report_child.Rmd', package = 'rexseek'), 
        quiet = T, options = list(params = list(...))
    )
    writeLines(child_output)
}

purrr::pmap(
    list(header = headers, mat_norm = mat_norms), 
    report_mat, 
    sample_class = sample_class, shape = 'label', color = 'label'
) %>% invisible()