wzhy2000 / fgwas Goto Github PK

Hi,
Sorry to bother you. when I loading genotype from plink files (bed,bim,fam),
I got an error about 【Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value when setting 'row.names】,however, I found these plink files can be loaded into the variable which I define. so should I go further analysis regardless of this error?
Thank you
Gang Xue

Thank you,
GangXue

Hi,

I am part of the Bioconda community, https://bioconda.github.io/, and would like to create a conda package for "fGWAS" for easier distribution and installation. However, in order to do this, the package needs to have a LICENSE file and a tagged release.
Can you please add these requirements so I can create the conda package?

Thank you,
Natasha

Hi,
I am running fGWAS for a longitudinal study and I have an issue that I don't know what happened. The number of sample is around 10,000 and the there are 4 observation time points. I got the following error.

obj.phe_EA <- fg.load.phenotype( file.phe.long_EA, file.phe.cov_EA, file.phe.time_EA, file.plot.pdf="/ddn/home2/r2725/projects/jeannette/data/curve.fitting_EA.pdf")
No curve or new curve type is specified, curve fitting is being performed.
Searching curve type ......

• [ 1 / 10 ] try curve: Logistic
• [ 2 / 10 ] try curve: Bi-Logistic
• [ 3 / 10 ] try curve: ABRK
• [ 4 / 10 ] try curve: Pharmacology
• [ 5 / 10 ] try curve: Exponential
• [ 6 / 10 ] try curve: Bi-Exponential
• [ 7 / 10 ] try curve: Power
• [ 8 / 10 ] try curve: Legendre2
• [ 9 / 10 ] try curve: Legendre3
• [ 10 / 10 ] try curve: Legendre4
  Curve Fitting Summary:
  type parm AIC AICc BIC SSE MSE RMSE R2
  1 Logistic 3 8799.088 5.400554 8815.891 162339.75 22.38243 4.731007 -0.1617916
  2 Bi-Logistic 6 8794.128 5.398092 8827.733 161452.51 22.26010 4.718061 -0.1554420
  3 ABRK 4 7405.987 4.704008 7428.391 80813.23 11.14204 3.337970 0.4216566
  4 Pharmacology 3 8799.688 5.400854 8816.491 162388.43 22.38914 4.731716 -0.1621400
  5 Exponential 2 8797.698 5.399855 8808.900 162389.27 22.38926 4.731729 -0.1621460
  6 Bi-Exponential 4 8800.852 5.401441 8823.256 162320.58 22.37978 4.730728 -0.1616544
  7 Power 2 8797.565 5.399788 8808.767 162378.44 22.38776 4.731571 -0.1620685
  8 Legendre2 3 8799.634 5.400827 8816.437 162384.06 22.38854 4.731653 -0.1621087
  9 Legendre3 4 8801.350 5.401690 8823.753 162360.95 22.38535 4.731316 -0.1619433
  10 Legendre4 5 8802.187 5.402114 8830.191 162266.58 22.37234 4.729941 -0.1612679
  Curve Type==> ABRK <==
  Parameter range estimation ......
  Searching covariance matrix .......
  *[ 1 / 13 ]: try covariance matrix: AR1
  *[ 1 / 13 ]: try covariance matrix: SAD1
  *[ 1 / 13 ]: try covariance matrix: ARMA(1,1)
  *[ 1 / 13 ]: try covariance matrix: ARH1
  *[ 1 / 13 ]: try covariance matrix: CS
  *[ 1 / 13 ]: try covariance matrix: CSH
  *[ 1 / 13 ]: try covariance matrix: VS
  *[ 1 / 13 ]: try covariance matrix: SI
  *[ 1 / 13 ]: try covariance matrix: FA1
  *[ 1 / 13 ]: try covariance matrix: FAH1
  *[ 1 / 13 ]: try covariance matrix: TOEP
  *[ 1 / 13 ]: try covariance matrix: TOEPH
  *[ 1 / 13 ]: try covariance matrix: HF
  Error in fg_dat_est(ret, curve.type, covariance.type, file.plot.pdf, options) :
  ? No covariance is fitted to this data.
  Calls: fg.load.phenotype -> fg_load_phenotype -> fg_dat_est
  In addition: There were 42 warnings (use warnings() to see them)
  Execution halted

I am wondering if you can help me to find a way to solve that issue? Thank you very much.

Hi @wzhy2000 ,

I have a question re the covariates file. I would like to integrate in the GWAS variables such as sex, and principal components of ancestry where each subject has one measure, but also two covariates, such as age at the time of weight where each subject has repeated measures. Can you please let me know if this is feasible and also how to format the covariate file accordingly?

Thank you!
Maria