## ------------------------------------------------------------------------
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")
## ------------------------------------------------------------------------
library("kma")
## ----eval=FALSE----------------------------------------------------------
# system.file("example", package="kma")
## ----, eval=FALSE--------------------------------------------------------
# system.file("pre-process", package = "kma")
#
## ------------------------------------------------------------------------
base_dir <- system.file("example", package="kma")
xprs_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/xprs_out/results.xprs"))
xprs_fnames
## ------------------------------------------------------------------------
sample_names <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", xprs_fnames) %>%
sub("xprs_out/results.xprs", "", .) %>%
gsub("/", "", .)
sample_names
## ------------------------------------------------------------------------
condition_names <- sub("[0-9]+", "", sample_names)
condition_names
## ------------------------------------------------------------------------
xprs <- read_express(xprs_fnames, sample_names, condition_names)
## ------------------------------------------------------------------------
names(xprs)
## ------------------------------------------------------------------------
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)
## ------------------------------------------------------------------------
ir <- newIntronRetention(xprs$tpm, intron_to_trans, xprs$condition,
xprs$uniq_counts)
## ------------------------------------------------------------------------
print(ir)
## ------------------------------------------------------------------------
head(ir$flat)
## ------------------------------------------------------------------------
ir <- ir %>%
filter_low_tpm(1) %>%
filter_perfect_psi() %>%
filter_low_frags(3)
colnames(ir$flat)
## ------------------------------------------------------------------------
zc_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/zero_coverage.txt"))
zc_samples <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", zc_fnames) %>%
sub("zero_coverage.txt", "", .) %>%
gsub("/", "", .)
zc_conditions <- sub("[0-9]+", "", zc_samples)
all_zc <- get_batch_intron_zc(zc_fnames, zc_samples, zc_conditions)
head(all_zc)
## ------------------------------------------------------------------------
ir <- summarize_zero_coverage(ir, all_zc)
## ------------------------------------------------------------------------
colnames(ir$flat)
## ------------------------------------------------------------------------
set.seed(42)
ir_test <- retention_test(ir)
head(ir_test)
## ------------------------------------------------------------------------
ir_test %>%
filter(qvalue <= 0.10) %>%
select(-c(pvalue))
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