Entering edit mode
nuch_tiwaporn
•
0
@nuch_tiwaporn-11974
Last seen 7.4 years ago
I am trying to read pedfile with read.pedfile ("filename.ped", p2g=TRUE) but I get an message "Error in read.pedfile("european_MTR_clean.ped", p2g = TRUE) : unused argument (p2g = TRUE)". The I tried to read a pedfile by read.pedfile ("filename.ped") but I got an error message "Error in read.pedfile("european_MTR_clean.ped") : object 'm' not found". Could someone give the solution?
Please edit your question to include the output of
traceback()immediately after the error occurs, andsessionInfo(). It seems like you asked a similar question on Biostars, and that the error about 'unused argument' is because you are actually invoking the snpStats function read.pedfile() instead of the trio function. Which one do you want to use? Trytrio::read.pedfile("filename.ped", p2g=TRUE).Thank you Martin. This is the result
> trio::read.pedfile("european_MTR_clean.ped", p2g=TRUE).
Error: unexpected symbol in "trio::read.pedfile("european_MTR_clean.ped", p2g=TRUE)."
> read.pedfile("european_MTR_clean.ped", p2g=TRUE)
Error in read.pedfile("european_MTR_clean.ped", p2g = TRUE) :
unused argument (p2g = TRUE)
> traceback()
1: read.pedfile("european_MTR_clean.ped", p2g = TRUE)
> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] session_1.0.3 car_2.0-25 GWASdata_1.3.2
[4] GWASTools_1.12.2 gdsfmt_1.2.2 ncdf_1.6.9
[7] Biobase_2.26.0 BiocGenerics_0.12.1 snpStats_1.16.0
[10] Matrix_1.2-6 survival_2.39-2 scrime_1.3.3
[13] haplo.stats_1.7.7 trio_3.4.0 BiocInstaller_1.16.5
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 chron_2.3-47 cluster_2.0.4
[4] codetools_0.2-14 colorspace_1.2-6 data.table_1.9.6
[7] DBI_0.4 DNAcopy_1.40.0 foreign_0.8-66
[10] Formula_1.2-1 ggplot2_2.1.0 grid_3.1.3
[13] gridExtra_2.2.1 gtable_0.2.0 GWASExactHW_1.01
[16] Hmisc_3.17-4 lattice_0.20-33 latticeExtra_0.6-28
[19] lme4_1.1-10 lmtest_0.9-34 MASS_7.3-45
[22] MatrixModels_0.4-1 mgcv_1.8-12 minqa_1.2.4
[25] multcomp_1.4-4 munsell_0.4.3 mvtnorm_1.0-5
[28] nlme_3.1-127 nloptr_1.0.4 nnet_7.3-12
[31] pbkrtest_0.4-4 plyr_1.8.3 polspline_1.1.12
[34] quantreg_5.21 quantsmooth_1.32.0 RColorBrewer_1.1-2
[37] Rcpp_0.12.4 rms_4.5-0 rpart_4.1-10
[40] RSQLite_1.0.0 sandwich_2.3-4 scales_0.4.0
[43] SparseM_1.7 splines_3.1.3 TH.data_1.0-7
[46] tools_3.1.3 zlibbioc_1.12.0 zoo_1.7-13
Warning messages:
1: closing unused connection 7 (MTR.ped)
2: closing unused connection 6 (european_MTR_clean.ped)
3: closing unused connection 5 (european_MTR_clean.ped)
4: closing unused connection 4 (european_MTR_clean.ped)
5: closing unused connection 3 (european_MTR_clean.ped)