sleuth_prep fail, read_kallisto , is(path, "character") is not TRUE #286
Description
new env
conda install --channel bioconda r-sleuth
Total: 245.0 MB
r-sleuth-0.30.0
python-3.11.5
r-base-3.6.1
...
R
library('sleuth')
samples = c("CK1","CK2","CK3","Y22_3HM1","Y22_3HM2","Y22_3HM3")
s2c <- data.frame(sample = samples, condition = rep(c("control", "case"), each = 3), path = paste("kallisto", samples, sep = "/"))
s2c
sample condition path
1 CK1 control kallisto/CK1
2 CK2 control kallisto/CK2
3 CK3 control kallisto/CK3
4 Y22_3HM1 case kallisto/Y22_3HM1
5 Y22_3HM2 case kallisto/Y22_3HM2
6 Y22_3HM3 case kallisto/Y22_3HM3
so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)
reading in kallisto results
dropping unused factor levels
.Error in read_kallisto(path, read_bootstrap = FALSE, max_bootstrap = max_bootstrap) :
is(path, "character") is not TRUE
read_kallisto("./kallisto/Y22_3HM3", read_bootstrap = FALSE, max_bootstrap = 100)
result:
kallisto object
transcripts: 4279
original number of transcripts: 4279
Original or Subset: Subsetbootstraps: 0
This read_kallisto("./kallisto/Y22_3HM3", read_bootstrap = FALSE, max_bootstrap = 100) can run !
why sleuth_prep(s2c, extra_bootstrap_summary = TRUE) fail?
How to do ?