nearbait error

[DimitrisZisis]

Dear Ramya,

I am producing bedgraph files from bam by using your script ( i modified the chr and i add it at the end cause my mapping files had only 1,2 etc instead of chr1, chr2 ) .
When i am trying to run 4Cker for mouse data i have an error sometimes .
this is the R input I used and error message :

my_obj = createR4CkerObjectFromFiles(files = c( "bedGraph_files/ESC_pcdhb19_1_fragments_chr_new.bedGraph",
"bedGraph_files/ESC_pcdhb19_2_fragments_chr_new.bedGraph",
"bedGraph_files/ESC_pcdhb19_3_fragments_chr_new.bedGraph",
"bedGraph_files/iPSC_Pcdhb19_1_fragments_chr_new.bedGraph",
"bedGraph_files/iPSC_Pcdhb19_2_fragments_chr_new.bedGraph",
"bedGraph_files/iPSC_Pcdhb19_3_fragments_chr_new.bedGraph"),
bait_chr="chr18",
bait_coord= 37483203,
bait_name = "Pcdhb19",
primary_enz = "AAGCTT",
samples = c("ESC_pcdhb19_1", "ESC_pcdhb19_2", "ESC_pcdhb19_3", "iPSC_Pcdhb19_1", "iPSC_Pcdhb19_2", "iPSC_Pcdhb19_3"),
conditions = c("ESC","iPSC"),
replicates = c(3,3),
species = "mm",
output_dir = "Mouse_4cker_Fragments_13_6_2018",
enz_file=enz_file)
nb_results=nearBaitAnalysis(my_obj,k=10)
[1] "Building adaptive windows..."
[1] "Normalizing counts..."
[1] "Generating synthetic samples...."
[1] "Parameter estimation....."
Error in if (as.character(windows[i, 1]) == chr & windows[i, 2] <= end & :
missing value where TRUE/FALSE needed

As because i have a 6bp cutter i use for nearbait k=10 and i have the error. If i change the k=5 it works .
I have seen that this happened again but i dont get what is the solution . Could you please help me with that ?

Best

Dimitris Zisis

[erinbrettmann]

I am getting this error, as well, but for me changing the value of k didn't fix it. Oddly, I have run the same files previously without getting the error, so I have no idea what's causing it. Can anyone tell me what this error means, and how to fix it?
Thanks,
Erin Brettmann

[rr1859]

Hi,

Sorry for the late reply. I think the issue is to do with merging the windows of the final output. I have modified the merge_windows.R file. Please try now and let me know if the problem is still there.

[erinbrettmann]

Thank you, that appears to have fixed it!