inst/doc/kma.R

In pachterlab/kma: KeepMeAround: Intron Retention Detection in RNA-Seq data

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system.file("pre-process", package="kma")

## ----, eval=FALSE--------------------------------------------------------
#  required_packages <- c("devtools", "data.table", "reshape2", "dplyr")
#  install.packages(required_packages)
#  devtools::install_github("http://github.com/pachterlab/kma")

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library("kma")

## ----eval=FALSE----------------------------------------------------------
#  system.file("example", package="kma")

## ----, eval=FALSE--------------------------------------------------------
#  system.file("pre-process", package = "kma")
#  

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base_dir <- system.file("example", package="kma")
xprs_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/xprs_out/results.xprs"))
xprs_fnames

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sample_names <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", xprs_fnames) %>%
    sub("xprs_out/results.xprs", "", .) %>%
    gsub("/", "", .)
sample_names

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condition_names <- sub("[0-9]+", "", sample_names)
condition_names

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xprs <- read_express(xprs_fnames, sample_names, condition_names)

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names(xprs)

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intron_to_trans <- data.table::fread(file.path(base_dir, "kma_pre-process_out",
    "intron_to_transcripts.txt"), data.table = FALSE)
head(intron_to_trans)

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ir <- newIntronRetention(xprs$tpm, intron_to_trans, xprs$condition,
    xprs$uniq_counts)

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print(ir)

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head(ir$flat)

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ir <- ir %>%
    filter_low_tpm(1) %>%
    filter_perfect_psi() %>%
    filter_low_frags(3)
colnames(ir$flat)

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zc_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/zero_coverage.txt"))
zc_samples <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", zc_fnames) %>%
    sub("zero_coverage.txt", "", .) %>%
    gsub("/", "", .)
zc_conditions <- sub("[0-9]+", "", zc_samples)
all_zc <- get_batch_intron_zc(zc_fnames, zc_samples, zc_conditions)
head(all_zc)

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ir <- summarize_zero_coverage(ir, all_zc)

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colnames(ir$flat)

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set.seed(42)
ir_test <- retention_test(ir)
head(ir_test)

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ir_test %>%
    filter(qvalue <= 0.10) %>%
    select(-c(pvalue))