Problem with "sleuth_prep" - 'kal_dirs' (sample_to_covariates) must be a data.frame

Question

[dr.fatemeh.askari]

I am running Sleuth, but facing the following issue when reaching the "so <- sleuth_prep". the Kir_dirs giving me the following results;

> kal_dirs
                                                                      SRR493367 
"~/Desktop/my_lab/Test/analysis/bears_iplant/results/paired/SRR493367/kallisto" 
                                                                      SRR493368 
"~/Desktop/my_lab/Test/analysis/bears_iplant/results/paired/SRR493368/kallisto" 


> so <- sleuth_prep(kal_dirs, s2c, ~ condition, target_mapping = t2g)

Error in sleuth_prep(kal_dirs, s2c, ~condition, target_mapping = t2g) : 
  'kal_dirs' (sample_to_covariates) must be a data.frame

How can fix this Error.

Answer 1

[zx8754]

Error is clear kal_dirs must be a data.frame with "sample" and "path" columns, maybe try:

kal_dirs_fixed <- data.frame(sample = names(kal_dirs), path = kal_dirs)

so <- sleuth_prep(kal_dirs_fixed, s2c, ~ condition, target_mapping = t2g)

sample_to_covariates a data.frame which contains a mapping from sample (a required column) to some set of experimental conditions or covariates. The column path is also required, which is a character vector where each element points to the corresponding kallisto output directory. The column sample should be in the same order as the corresponding entry in path