object 'post_post.processing' not found

[kallol0729]

Hi,

I was trying the tutorial to check if I can properly run the package. However, I am getting an error message as below:

Error in RTIGER(expDesign = expDesign, outputdir = output_dir, seqlengths = chr_len, :
object 'post_post.processing' not found

I tried changing the 'rigidity' parameter and it did not help.

My script is given below:

library("RTIGER")
library("Gviz")
library("rtracklayer")

#setupJulia()
sourceJulia()

Get paths to example allele count files originating from a

cross between Col-0 and Ler accession of the A.thaliana

file_paths = list.files(system.file("extdata", package = "RTIGER"), full.names = TRUE)

Get sample names

sampleIDs <- basename(file_paths)

Create the expDesign object

expDesign = data.frame(files=file_paths, name=sampleIDs)

print(expDesign)

Get chromosome lengths for the example data included in the package

chr_len <- RTIGER::ATseqlengths
names(chr_len) <- c('Chr1' , 'Chr2', 'Chr3', 'Chr4', 'Chr5')
print(chr_len)
output_dir <- "C:/my_test_data"

myres = RTIGER(expDesign = expDesign,
outputdir = output_dir,
seqlengths = chr_len,
rigidity = 20,
save.results = TRUE)

[rfael0cm]

Hi Kallo,
could you run it with verbose = TRUE and print the results again here?. Also, are you sure you have the latest version installed?
Best,
Rafael

[kallol0729]

Hi Rafael!

Thank you for getting back to me so quickly. I could successfully run on the example data by adding 'autotune = TRUE'. I have also tried adding 'verbose = TRUE' with 'autotune = FALSE' but it yields the same error.

However, when I try to implement it on my dataset it gives me a different error:

**Loading data and generating RTIGER object.
Using 2 states for fitting.
[1] "Loading file: C:/Users/Mahmood Hasan/OneDrive - University of Florida/Doctoral studies/mop1_project/rtiger/WT/W5.txt"

Fitting the parameters and Viterbi decoding.
post processing value is: TRUE
R value autotune is: TRUE
Fitting an RTIGER object with the R provided by the user.
Optimizing the R parameter.
Error in params[["paraBetaAlpha"]][state, 1] : subscript out of bounds**

My script is here:

library("RTIGER")
library("Gviz")
library("rtracklayer")
setupJulia()
sourceJulia()

file_paths <- list.files("C:/Users/Mahmood Hasan/OneDrive - University of Florida/Doctoral studies/mop1_project/rtiger/WT", full.names = TRUE)
sampleIDs <- basename(file_paths)
expDesign = data.frame(files=file_paths, name=sampleIDs)

print(expDesign)

chromosome_lengths <- c(308452471, 243675191, 238017767, 250330460, 226353449,
                        181357234, 185808916, 182411202, 163004744, 152435371)

chromosome_names <- c("Chr1", "Chr2", "Chr3", "Chr4", "Chr5",
                      "Chr6", "Chr7", "Chr8", "Chr9", "Chr10")

chr_len <- setNames(chromosome_lengths, chromosome_names)


output_dir <- "C:/Users/Mahmood Hasan/OneDrive - University of Florida/Doctoral studies/mop1_project/rtiger"
myres <- RTIGER(expDesign = expDesign,
                outputdir = output_dir,
                seqlengths = chr_len,
                autotune=TRUE,
                rigidity = 8,
                nstates=2,
                save.results = TRUE)

Best regards,
Mahmood

[rfael0cm]

Dear Mahmood,
thank you very much for sending me the code and the output. I now see which is the problem. Our autotune algorithm has been only developed for 3 states, which we thought would be the most common.
For other number of states, please, run autotune = TRUE but using three states and use the R value obtained in this process as guide to fit the RTIGER object with 2 states and autotune = FALSE.
Does it make sense?
Please let me know if this fixes the problem.
Best,
Rafael

[kallol0729]

Hi Rafael!

Thank you so much for your kind response. I will try that and let you know the outcome.

Best,
Mahmood