library(fluidgr)
library(magrittr)
library(dplyr)
library(stringr)
path_to_data <- system.file("extdata", "sample-fluidigm-run.csv",
package = "fluidgr",
mustWork = TRUE)
normalizers <- c("normalizer1",
"normalizer2",
"normalizer3")
dat <- read_fluidigm(path = path_to_data,
simplify = TRUE) %>%
filter(!sample_name %>% str_detect("Mix")) %>%
filter(sample_name != "H20") %>%
filter(target_name != "normalizer1bis")
normalizers <- c("normalizer1",
"normalizer2",
"normalizer3")
fluidigm_expr <-
dat %>%
normalize(normalizers = normalizers)
use_data(fluidigm_expr, overwrite = T)
# Scale -------------------------------------------------------------------
scaled_fluidigm <-
fluidigm_expr %>%
scale_fluidigm(.group = target_name)
# Explicit categorical variables ------------------------------------------
scaled_fluidigm<-
scaled_fluidigm %>%
# make species explicit
mutate(species = str_split_fixed(string = sample_name,
pattern = "-",
n = 2)[, 1]) %>%
# make stage explicit
mutate(stage = str_sub(string = sample_name,
start = 3,
end = 4)) %>%
# make replicate explicit
mutate(replicate = str_sub(string = sample_name,
start = 5,
end = 6))
# Save --------------------------------------------------------------------
use_data(scaled_fluidigm, overwrite = TRUE)
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