Open kallol0729 opened 8 months ago
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
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
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
Hi Rafael!
Thank you so much for your kind response. I will try that and let you know the outcome.
Best, Mahmood
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)