Displaying 4 results from an estimated 4 matches for "snp6".
Did you mean:
snp
2011 Mar 10
1
snp-chip table
Dear R helpers
I have a table and i need to make new table
table1:
sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10
snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1
7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1
0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0
0 1
I have table2
sire snp1 snp2 snp3 snp4 snp...
2009 Feb 27
5
Filtering a dataset's columns by another dataset's column names
...e in common with the other dataset.
Here is a toy example (my real datasets have hundreds of columns):
Dataset 1:
Individual SNP1 SNP2 SNP3 SNP4 SNP5
1 A G T C A
2 T C A G T
3 A C T C A
Dataset 2:
Individual SNP1 SNP3 SNP5 SNP6 SNP7
4 A T T G C
5 T A A G G
6 A A T C G
I want Dataset1 to have only columns that are also represented in Dataset 2, i.e., I want to generate a new Dataset 3 that looks like this:
Individual SNP1 SNP3 SNP5
1 A T A
2 T A T...
2009 Sep 01
1
permutation and reshuffling
...individuals and creating a loop that will
randomly simulate it for 10000 times *(permutation)*. I also need to find
how I keep the information (p value for each SNP) gathered for all the 10000
iterations.
My data set looks like this (n=500):
Individual #
Phenotype
SNP1
SNP2
SNP3
SNP4
SNP5
SNP6
SNP7
SNP8
SNP9
SNP10
SNP11
SNP12
1
0
T
T
G
G
A
C
G
T
A
A
T
C
2
1
A
T
C
G
A
C
G
T
A
G
T
C
Many thanks,
Jonathan
[[alternative HTML version deleted]]
2011 Jan 03
0
Using PCA to correct p-values from snpMatrix
...(0,1,0,-1,-1,1,1,-1,0,1,1,0,0,1,0,-1,-1,NA,0,-1,0,0,1,0),
nrow=3,
dimnames = list(
c("bob", "frita", "trudy"),
c("snp1", "snp2", "snp3", "snp4", "snp5","snp6", "snp7",
"snp8")
)
)
# phenotype data - resistant or susceptible to zombie infection
phenotype.data = matrix(
c("bob", "frita", "trudy",
"resistant", "susceptible", "re...