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It took me quite a lot to understand stopifnot(is(path, "character")) crashes caused by the following code:
base <- file.path("/home", "rstudio", "samples")
samples <- c("GSM1944768", "GSM1944769")
quant <- "transcripts_quant"
pathes <- map_chr(samples, function(s) str_c(base, "/", s, "/", quant, "/"))
prepare_fish_for_sleuth(pathes)
conditions <- c("one", "two")
s2c = data.frame(
sample = samples,
condition = conditions,
path = pathes
#will not work until I will put stringsAsFactors=FALSE
)
so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)
I suggest that it should work even if strings are factors in order not to confuse users
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