poissonfish/ipat

iPat allows you to perform GWAS and GS with drags and clicks!

ipat's Issues

unable to install r package-error package ‘http://zzlab.net/iPat/iPat_installation.r’ is not available (for R version 4.0.0)

Blank "run" screen

Hi, I'm a windows user and I've installed R 3.4.3 with all the necessary packages from the link and also java 8 update 161.

I downloaded iPat, demo data and all the steps are working (using plink demo files and just GWAS) up until "run" where it stops and outputs a blank word file and an .err file.

Any ideas what I'm doing wrong?
Many thanks

Imposible to run the project

Hi,
I am working in MAC. After downloaded the program and the R packages, I have tried to train with the demo data but when I try to run the project the command is inactive (in grey). I have draged the GWAS method with default settings but the command remains inactive. Thank you for your help.
Estefania.

Error in library(R.utils): there is no package called 'R.utils'

Hello!

I was trying to analyze my data using the PLINK method in iPat, but got the following error:

Error in library(R.utils): there is no package called 'R.utils'

Thanks!

about covariates

If my fixed effects are gender and season,(like 0 for female, 1 for male and 0 for winter 1 for summer
Taxa gneder season
ID1 1 1
ID2 1 1
ID3 0 0
they will be treated as covariates in the BGLR method. How can it be converted into a format recognized by ipat
Taxa Cov1 Cov2
ID_1 3.617538 -0.9368706
ID_2 0.888413 -0.0546190
ID_3 -1.276830 0.2140963)
thanks a lot !

iPat: SSL connection error

I am encountering following issue with iPat:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection to 'http://zzlab.net/iPat/RiPat_main.r'
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
URL 'https://zzlab.net/iPat/RiPat_main.r': status was 'SSL connect error'
Execution halted

How can I overcome/solve this issue? Thanks in advance for your help.

iPat for mac os is not available somehow

Hi there. The download hyperlink for Mac-os does not work. Could you please get it shared again? Thanx!

ipat.exe not executable

Hi there,
I'm a windows user (Dell T7500)and I've installed R 3.5.0 with all the necessary packages from the link and also java 10 .
When I double click ipat.exe , the computer just has no reaction. It seems like the ipat.exe is not executable. Any help ?

Wen

windows can't open ipat.exe

Hi，I download the ipat windows version, but nothing happened when I tried to open the executable file even though I used two computers and admistrator identity to run.

One of my PCs information as below:
Windows 10
Intel(R) Core(TM) i5-6300U cPU @2.40GHz 2.50 GHz，x64
16.0 GB RAM

GS on

Dear James,

I hope you can give guidance on genomic selection application.

I have a Genome wide association population (Genotype & Phenotype) that was used to develop a predictive model. I wish to you this to make GEBV prediction in F6 bi-parental breeding populations based on genotype values. Could you kindly detail how data should be inputted into iPat so I can define the GWAS population as the training set to calculate the GEBV in these new F6 populations to ultimately apply selection selection on them. ie. I wish to use the GWAS population to define marker effects and apply these to the non-phenotyped F6s to select them based on GEBV.

thank you kindly,

James

Error issue while runnning GWAS

Hi!

I am Rezha.

It is really nice to know your useful application. Unfortunately, I am encountering problem as follows:

1. The run was interrupted by an error.

2. Some packages seemed unistalled.

Could you please help me regarding these issues?

Thank you.

problem running in windows

James

On two independent computers we have encountered running iPat.

We have downloaded the demo files but does not work. Is the script compatible with updated versions of R?

We are running R 4.2.2

Thanking you for assistance in advance.

James

Demo file cannot run

Dear James
I am a windows user and downloaded the latest R3.6.3,
then using source ("http://zzlab.net/iPat/iPat_installation.r") to install the packages that ipat need.
All the packages are installed and the required packages are carefully checked, but when I run the 'case2 demo file', the running box is blank and there is nothing, what is wrong?
Thanks a lot!!

Error in if (args[i] == "-wd") { : argument is of length zero

Hi I am getting an error associated with the launcher:

Error in if (args[i] == "-wd") { : argument is of length zero

I had the iPat installed and working fine then updated R to version 4.2.2

James

Tutorial

Hi James

Could you please add some tutorials on using different combinations of data formats and methods?

Thank you.

Zhiwu

iPat Error using BGLR: "Error in file(description = fname, open = "w") : cannot open the connection"

Error in file(description = fname, open = "w") :
cannot open the connection
Calls: tryCatch -> tryCatchList -> tryCatchOne ->
In addition: Warning messages:
1: package 'BGLR' was built under R version 3.5.2
2: package 'rrBLUP' was built under R version 3.5.2
3: package 'data.table' was built under R version 3.5.2
4: package 'magrittr' was built under R version 3.5.2
5: package 'ggplot2' was built under R version 3.5.2
6: In doTryCatch(return(expr), name, parentenv, handler) :
NAs introduced by coercion
7: In file(description = fname, open = "w") :
cannot open file 'iPat_Project_BGLR_ETA_1_varB.dat': Permission denied
Execution halted

Error in GAPIT.Main(Y = ic_Y, GD = DP$GD[, -1], GM = DP$GM, KI = ic_KI, : 找不到对象'Compression0'

when I perform GWAS by GAPIT method, there is an error as follow: Error in GAPIT.Main(Y = ic_Y, GD = DP$GD[, -1], GM = DP$GM, KI = ic_KI, : 找不到对象'Compression0'. I have read the original code and found there is "Compression=Compression0" in 767th line in GAPIT.Main function. Please give me help!