Question: meaning of "hiseq_info.txt" in Sleuth
0
gravatar for dr.fatemeh.askari
7 weeks ago by
dr.fatemeh.askari20 wrote:

Hey all,

In sleuth, what is the meaning of "hiseq_info.txt"???? is it the same as experimental design info.

I am running sleuth as follows;

find the data

> getkdir <- function(id) file.path(base_dir, "results", id, "kallisto")
> base_dir <- system.file("extdata", "", package="sleuthData")
> sample_id <- dir(file.path(base_dir,"results"))
> kal_dirs <- sapply(sample_id, getkdir)
> base_dir <- "~/Desktop/my_lab/Test"

mapping sample

> s2c <- read.table(file.path(base_dir, "meta_data.txt"), header = TRUE, stringsAsFactors=FALSE)


> s2c <- dplyr::select(s2c, sample=run_accession, condition)

what is {sample=run_accession}?? what it means exactly? did I miss a step here? or I need to have sleuth installed to work?

Error: Can't subset columns that don't exist.
x Column `run_accession` doesn't exist.
Run `rlang::last_error()` to see where the error occurred.
> `rlang::last_error()`
Error: object 'rlang::last_error()' not found
> rlang::last_error()
<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `run_accession` doesn't exist.
Backtrace:
  1. dplyr::select(s2c, sample = run_accession, condition)
  2. dplyr:::select.data.frame(s2c, sample = run_accession, condition)
  3. tidyselect::eval_select(expr(c(...)), .data)
  4. tidyselect:::eval_select_impl(...)
 12. tidyselect:::vars_select_eval(...)
 13. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 14. tidyselect:::eval_c(expr, data_mask, context_mask)
 15. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 16. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 17. tidyselect:::as_indices_sel_impl(...)
 18. tidyselect:::as_indices_impl(x, vars, strict = strict)
 19. tidyselect:::chr_as_locations(x, vars)
 20. vctrs::vec_as_location(x, n = length(vars), names = vars)
 22. vctrs:::stop_subscript_oob(...)
 23. vctrs:::stop_subscript(...)
Run `rlang::last_trace()` to see the full context.
>
rna-seq • 141 views
ADD COMMENTlink modified 28 days ago by Biostar ♦♦ 20 • written 7 weeks ago by dr.fatemeh.askari20

Do you try to run your data or the example data?

ADD REPLYlink written 28 days ago by ATpoint40k
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