Entering edit mode
@johannes-gulmann-madsen-3350
Last seen 9.6 years ago
Hello
Im a new user of Bioconductor and therefore also a new user of the
package
GeneticsBase. I have a dataframe looking like this (only a tiny bit of
it):
> b[1:10,]
SNP.Name Sample.ID Allele1...Top Allele2...Top
GC.Score
1 0_A2M_DS066406.1_15 602358305 G G
0.8607
2 0_A2M_DS068238.1_4 602358305 G G
0.8311
3 0_AARSL_DS061819.1_2 602358305 G G
0.6840
4 0_ABCA1_DS062937.1_32 602358305 G G
0.7499
5 0_ABCA1_DS073864.1_41_2 602358305 A A
0.7900
6 0_ABCA1_DS073864.1_41 602358305 G G
0.7383
7 0_ABCA1_DS078984.1_39 602358305 A A
0.8360
8 0_ABCA1_DS082793.1_19 602358305 G G
0.8440
9 0_ABCC10_DS066718.1_3 602358305 C C
0.8859
10 0_ABCC6_DS063353.1_20 602358305 A C
0.6117
Its of class 'data.frame' and i want it converted to a 'geneset' using
as.geneSet.
So i tried:
b2 <- as.geneSet(b, gene.columns=c("Allele1...Top", "Allele2...Top",
format=c("adjacent")), because the "Allele1...Top" and "Allele2...Top"
are
(combined, thats why i want to use format=c("adjacent"), is that
wrong?) my
genotypes, but it won't work. Does any of you have any experience
using
'as.geneSet', i can't find any examples on the net that looks like
mine? My
idea of the dataset is that i want to genotype each 'Sample.ID' like
this (a
simple example):
Sample.ID 1:
SNP1: AA 0
AC 1
CC 2
Sample.ID 2:
SNP1: AA 0
AC 1
CC 2
So I want to make sure that the same SNP on different Sample.ID's is
genotyped
the same way (like illustrated above).
Hope you can help me.
Regards Johannes
