When I run the descriptive scan, my results come as follow :
as you see the first column which is the SNPnames column comes without a column names
I need to save my results as data frame, and the snp clumn is missing
I inspected the different slots of my gwa.class, and there is no snpnames column.
is it possible to recover it?
Code: Select all
descriptives.scan(coxresults_BRIT_1, top=20)
Chromosome Position Strand A1 A2 N effB se_effB chi2.1df P1df Pc1df effAB effBB chi2.2df P2df
rs777 3 57555793 u A G 409 0.5936605 0.12347777 23.11526
rs462 3 57559004 u G A 409 0.5936605 0.12347777 23.11526
rs672 3 57578276 u C A 409 0.5936605 0.12347777 23.11526
> str(coxresults_BRIT_1)
Formal class 'scan.gwaa' [package "GenABEL"] with 7 slots
..@ results :'data.frame': 468913 obs. of 10 variables:
.. ..$ N : num [1:468913] 409 409 408 409 409 409 409 409 409 409 ...
.. ..$ effB : num [1:468913] -0.1044 -0.0109 -0.1515 -0.1022 0.0221 ...
.. ..$ se_effB : num [1:468913] 0.145 0.101 0.108 0.116 0.106 ...
.. ..$ chi2.1df: num [1:468913] 0.5154 0.0117 1.9784 0.7774 0.0435 ...
.. ..$ P1df : num [1:468913] 0.473 0.914 0.16 0.378 0.835 ...
.. ..$ Pc1df : num [1:468913] 0.476 0.914 0.163 0.382 0.836 ...
.. ..$ effAB : logi [1:468913] NA NA NA NA NA NA ...
.. ..$ effBB : logi [1:468913] NA NA NA NA NA NA ...
.. ..$ chi2.2df: logi [1:468913] NA NA NA NA NA NA ...
.. ..$ P2df : logi [1:468913] NA NA NA NA NA NA ...
..@ dimresults: int [1:2] 468913 10
..@ annotation:'data.frame': 468913 obs. of 5 variables:
.. ..$ Chromosome: Factor w/ 22 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ Position : num [1:468913] 765555 798789 152358 125855 ...
.. ..$ Strand : Factor w/ 1 level "u": 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ A1 : Factor w/ 3 levels "A","C","G": 3 3 2 1 1 3 3 1 3 3 ...
.. ..$ A2 : Factor w/ 3 levels "A","C","G": 1 1 1 3 2 1 1 3 1 1 ...
..@ lambda :List of 2
.. ..$ estimate: num 1.02
.. ..$ se : num 2.31e-05
..@ idnames : chr [1:409] "deadkf04" "deadkf05" "deadkf06" "deadkf07" ...
..@ call : language mlreg(formula = GASurv(survivaldataBRIT@phdata$ObsMonths, survivaldataBRIT@phdata$Status) ~ 1, data = qcGWAS_Brit)
..@ family : chr "guess"