I am not sure what I am suppose to run from your codes.
Can you just send me lines of codes which I should run? (without part
where you are loading your data frames)
(assuming my files are as I showed them)
Or the whole idea was to remove sep=" " from everywhere?
On Fri, Apr 10, 2020 at 7:01 PM R
On 2020-04-10 18:46 -0500, Ana Marija wrote:
> so if I understand correctly you would just remove sep=" " from my codes?
>
> Thank you so much for working on this.
> Is there is any chance you can change my original code (pasted bellow)
> with changes you think should work?
>
> library(SNPRelate)
so if I understand correctly you would just remove sep=" " from my codes?
Thank you so much for working on this.
Is there is any chance you can change my original code (pasted bellow)
with changes you think should work?
library(SNPRelate)
# get PLINK output
plink.genome <- read.table("plink.geno
On 2020-04-10 17:05 -0500, Ana Marija wrote:
> it didn't work unfortunately with your
> example:
>
> > plink.genome[idx,]
> character(0)
Hi! Perhaps csv formatting are better
suited for these emails ... the two
ibdlist lines I added still matches in
this example, added lookup for kinship
..
it didn't work unfortunately with your example:
> plink.genome[idx,]
character(0)
here is my whole:
plink.genome <- read.table("plink.genome", header=TRUE)
FID1 IID1 FID2 IID2 RTEZ Z0 Z1 Z2
PI_HAT PHE DST PPC RATIOIBS0IBS1IBS2 HOMHOM
HETHET
On 2020-04-10 15:38 -0500, Ana Marija wrote:
| Hi,
|
| I have this code:
Dear Ana,
none of the ID tuples in the head
outputs you provided matches, so I added
two lines in ibdlist that matches up;
perhaps if you provided more lines that
would have matched in a pastebin
somewhere ...
optio
On Fri, Apr 10, 2020 at 2:54 PM Duncan Murdoch wrote:
> On 10/04/2020 3:46 p.m., Ana Marija wrote:
> > I have in current directory from
> > where I would run this function a
> > file named output4.bed
>
> Just use "output4.bed" as the
> filename. The system.file() function
> is for working out
Hi,
I have this code:
library(SNPRelate)
# get PLINK output
plink.genome <- read.table("plink.genome", header=TRUE)
> head(plink.genome)
FID1 IID1FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST
1 fam1054 G1054 fam1054 G700 OT 0 0.0045 0.9938 0.0017 0.4986 -1 0.839150
2 fa
Got it, thanks!
On Fri, Apr 10, 2020 at 2:54 PM Duncan Murdoch wrote:
>
> On 10/04/2020 3:46 p.m., Ana Marija wrote:
> > Hello,
> >
> > I would like to try this example in this link:
> > https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS
> >
> > for example this
On 10/04/2020 3:46 p.m., Ana Marija wrote:
Hello,
I would like to try this example in this link:
https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS
for example this line:
bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate")
I have in c
I tried to do this but I got this error:
> bed.fn <- system.file("output4.bed", package="SNPRelate")
> dim(bed.fn)
NULL
> fam.fn <- system.file("output4.fam", package="SNPRelate")
> bim.fn <- system.file("output4.bim", package="SNPRelate")
> snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")
Star
Hello,
I would like to try this example in this link:
https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS
for example this line:
bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate")
I have in current directory from where I would run this
Thank you so much!
On Fri, Apr 10, 2020 at 12:00 PM Rasmus Liland wrote:
>
> On 2020-04-10 11:15 -0500, Ana Marija wrote:
> > I have a data frame (tot) with about
> > 2000 columns. How can I extract from
> > it all strings that start with E14?
> >
> > I tried this:
> > e14 <- sapply(tot, function
"I thought: why make this overly complicated,..."
Indeed, though "complicated" is in the eyes of the beholder.
One wonders whether any of this is necessary, though: see ?apply , as in
apply(a, 1, whatever...)
to do things rowwise.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind i
On 2020-04-10 11:15 -0500, Ana Marija wrote:
> I have a data frame (tot) with about
> 2000 columns. How can I extract from
> it all strings that start with E14?
>
> I tried this:
> e14 <- sapply(tot, function(x) grepl("^E14", x))
>
> but this returns me just TRUE and
> FALSE vector, how do I g
Dear Ana
Would it not be possible to use grep instead of grepl and get the values
using the value = TRUE parameter?
Michael
On 10/04/2020 17:15, Ana Marija wrote:
Hello,
Hello,
I have a data frame (tot) with about 2000 columns. How can I extract
from it all strings that start with E14?
I
Hello,
Hello,
I have a data frame (tot) with about 2000 columns. How can I extract
from it all strings that start with E14?
I tried this:
e14 <- sapply(tot, function(x) grepl("^E14", x))
but this returns me just TRUE and FALSE vector, how do I get actual
strings that start with E14?
Thanks
Ana
On 2020-04-09 18:00 +, aiguo li wrote:
| That is awesome! Thanks.
Dear AiGuo,
I thought: why make this overly
complicated, when this is also
possible:
a <- matrix(LETTERS[1:16], nrow=4)
X <- split(x=a[,-1], f=a[,1])
lapply(X=X, FUN=as.factor)
Best,
Rasmus
_
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