Post by forevertl on Mar 17, 2020 16:18:43 GMT
HI,
I'd like to ask a question. When I run cojo analysis, I got error information as below. It said my first line has invalid sample size. I saw previous post mentioned the same error and people suggestion to read the this data in R. I did it and didn't find problem as below. Do you have any idea how to fix it?thank you very much.
Lin
Error: invalid sample size in line:
"rs2379981 chr22_16549902_G_A_b38 chr22 16549902 A G 0.9428 0.3511 -0.93245775 -0.004 0.004289738619391596 487409"
> r=read.table("chr22_dev2.txt",head=T,as.is=T)
> dim(r)
[1] 31397 12
ltong@bsdad.uchicago.edu@phs-vms19:~/phsfiles/users/ltong>head chr22_dev2.txt
SNP panel_variant_id chromosome position A1 A2 freq p zscore b se N
rs2379981 chr22_16549902_G_A_b38 chr22 16549902 A G 0.9428 0.3511 -0.93245775 -0.004 0.004289738619391596 487409
rs5747620 chr22_16551808_T_C_b38 chr22 16551808 C T 0.43520000000000003 0.7884 -0.26838887-0.0006 0.0022355621746204266 487409
rs9605879 chr22_16569017_G_A_b38 chr22 16569017 A G 0.4677 0.3606 -0.9142224 -0.0018 0.001968886303896563 590475
rs9605903 chr22_16573830_T_C_b38 chr22 16573830 C T 0.2663 0.1184 -1.5615247 -0.0033 0.002113319050838845 583339
rs5746647 chr22_16576248_G_T_b38 chr22 16576248 T G 0.9424 0.3027 -1.0306606 -0.0041 0.003978031064303071 590884
rs4819760 chr22_16576707_G_A_b38 chr22 16576707 A G 0.2669 0.09748 -1.6571953 -0.0035 0.0021120020901248364 581175
rs9605923 chr22_16584189_T_A_b38 chr22 16584189 A T 0.2659 0.1292 -1.5172641 -0.0032 0.0021090592873798273 579534
rs5747968 chr22_16586614_G_T_b38 chr22 16586614 T G 0.6639 0.3185 0.99754506 0.002 0.0020049219560984268 588490
rs13053626 chr22_16589219_A_G_b38 chr22 16589219 G A 0.025800000000000045 0.981 0.023815220.0001 0.004198995393212369 592282
I'd like to ask a question. When I run cojo analysis, I got error information as below. It said my first line has invalid sample size. I saw previous post mentioned the same error and people suggestion to read the this data in R. I did it and didn't find problem as below. Do you have any idea how to fix it?thank you very much.
Lin
Error: invalid sample size in line:
"rs2379981 chr22_16549902_G_A_b38 chr22 16549902 A G 0.9428 0.3511 -0.93245775 -0.004 0.004289738619391596 487409"
> r=read.table("chr22_dev2.txt",head=T,as.is=T)
> dim(r)
[1] 31397 12
ltong@bsdad.uchicago.edu@phs-vms19:~/phsfiles/users/ltong>head chr22_dev2.txt
SNP panel_variant_id chromosome position A1 A2 freq p zscore b se N
rs2379981 chr22_16549902_G_A_b38 chr22 16549902 A G 0.9428 0.3511 -0.93245775 -0.004 0.004289738619391596 487409
rs5747620 chr22_16551808_T_C_b38 chr22 16551808 C T 0.43520000000000003 0.7884 -0.26838887-0.0006 0.0022355621746204266 487409
rs9605879 chr22_16569017_G_A_b38 chr22 16569017 A G 0.4677 0.3606 -0.9142224 -0.0018 0.001968886303896563 590475
rs9605903 chr22_16573830_T_C_b38 chr22 16573830 C T 0.2663 0.1184 -1.5615247 -0.0033 0.002113319050838845 583339
rs5746647 chr22_16576248_G_T_b38 chr22 16576248 T G 0.9424 0.3027 -1.0306606 -0.0041 0.003978031064303071 590884
rs4819760 chr22_16576707_G_A_b38 chr22 16576707 A G 0.2669 0.09748 -1.6571953 -0.0035 0.0021120020901248364 581175
rs9605923 chr22_16584189_T_A_b38 chr22 16584189 A T 0.2659 0.1292 -1.5172641 -0.0032 0.0021090592873798273 579534
rs5747968 chr22_16586614_G_T_b38 chr22 16586614 T G 0.6639 0.3185 0.99754506 0.002 0.0020049219560984268 588490
rs13053626 chr22_16589219_A_G_b38 chr22 16589219 G A 0.025800000000000045 0.981 0.023815220.0001 0.004198995393212369 592282