[R] add a list name into the list content in a new output
Chel Hee Lee
chl948 at mail.usask.ca
Tue Jan 20 16:48:48 CET 2015
Hi Joshua,
You may use 'do.call()'. Please see the output in below:
> result <- lapply(names(op), function(x){
+ col1 <- x
+ col2 <- row.names(op[[x]])
+ mat <- op[[x]]
+ row.names(mat) <- NULL
+ rval <- cbind(col1, col2, mat)
+ names(rval) <- c("trait", "locus", names(mat))
+ rval
+ })
> result
[[1]]
trait locus chr pos ci.low ci.high lod
1 bp c7.loc45 7 47.7 36.71 56.7 6.11
2 bp c15.loc8 15 12.0 3.96 22.8 5.29
[[2]]
trait locus chr pos ci.low ci.high lod
1 hr c2.loc54 2 59.8 14.8 87.8 4.19
2 hr D15MIT184 15 22.8 12.0 36.0 3.15
[[3]]
trait locus chr pos ci.low ci.high lod
1 bw c15.loc16 15 20 11 30 6.75
[[4]]
trait locus chr pos ci.low ci.high lod
1 heart_wt c12.loc49 12 51.2 28.2 62.2 3.65
> do.call(rbind, result)
trait locus chr pos ci.low ci.high lod
1 bp c7.loc45 7 47.7 36.71 56.7 6.11
2 bp c15.loc8 15 12.0 3.96 22.8 5.29
3 hr c2.loc54 2 59.8 14.80 87.8 4.19
4 hr D15MIT184 15 22.8 12.00 36.0 3.15
5 bw c15.loc16 15 20.0 11.00 30.0 6.75
6 heart_wt c12.loc49 12 51.2 28.20 62.2 3.65
>
Is this what you are looking for? I hope this helps.
Chel Hee Lee
On 1/20/2015 9:23 AM, Shuhua Zhan wrote:
> Hi Chel,
> Thank you very much for your help!
> I'm sorry I did not post my wanted output correctly. I only want the colnames of the data frame occur once as a table:
> trait locus chr pos ci.low ci.high lod
> bp c7.loc45 7 47.7 36.71 56.7 6.11
> bp c15.loc8 15 12.0 3.96 22.8 5.29
> hr c2.loc54 2 59.8 14.8 87.8 4.19
> hr D15MIT184 15 22.8 12.0 36.0 3.15
> bw c15.loc16 15 20 11 30 6.75
> heart_wt c12.loc49 12 51.2 28.2 62.2 3.65
> How to add command to your script to scape those colnames?
> Thanks again,
> Joshua
>
> ----- Original Message -----
> From: "Chel Hee Lee" <chl948 at mail.usask.ca>
> To: "Shuhua Zhan" <szhan at uoguelph.ca>, "r-help" <r-help at r-project.org>
> Sent: Monday, January 19, 2015 10:44:23 PM
> Subject: Re: [R] add a list name into the list content in a new output
>
> I am just using the first two components of your output.
>
> > op
> $bp
> chr pos ci.low ci.high lod
> c7.loc45 7 47.7 36.71 56.7 6.11
> c15.loc8 15 12.0 3.96 22.8 5.29
>
> $hr
> chr pos ci.low ci.high lod
> c2.loc54 2 59.8 14.8 87.8 4.19
> D15MIT184 15 22.8 12.0 36.0 3.15
>
> >
> > result <- lapply(names(op), function(x){
> + col1 <- x
> + col2 <- row.names(op[[x]])
> + mat <- op[[x]]
> + row.names(mat) <- NULL
> + rval <- cbind(col1, col2, mat)
> + names(rval) <- c("trait", "locus", names(mat))
> + rval
> + })
> >
> > result
> [[1]]
> trait locus chr pos ci.low ci.high lod
> 1 bp c7.loc45 7 47.7 36.71 56.7 6.11
> 2 bp c15.loc8 15 12.0 3.96 22.8 5.29
>
> [[2]]
> trait locus chr pos ci.low ci.high lod
> 1 hr c2.loc54 2 59.8 14.8 87.8 4.19
> 2 hr D15MIT184 15 22.8 12.0 36.0 3.15
>
> >
>
> Is this what you are looking for? I hope this helps.
>
> Chel Hee Lee
>
>
> On 01/19/2015 02:14 PM, Shuhua Zhan wrote:
>> Dear All,
>> I'd like to add a list name into the list contents to make a new output. The list is a list of data.frame derived from summary command in Rqtl. I want to add this list name to the data frame with a given column name such as "trait" and output this entire list as a table tab delimited as below.
>> Here is the list generated by summary command in Rqtl:
>>> summary(out.all, threshold=3, format="tabByCol")
>> bp:
>> chr pos ci.low ci.high lod
>> c7.loc45 7 47.7 36.71 56.7 6.11
>> c15.loc8 15 12.0 3.96 22.8 5.29
>>
>> hr:
>> chr pos ci.low ci.high lod
>> c2.loc54 2 59.8 14.8 87.8 4.19
>> D15MIT184 15 22.8 12.0 36.0 3.15
>>
>> bw:
>> chr pos ci.low ci.high lod
>> c15.loc16 15 20 11 30 6.75
>>
>> heart_wt:
>> chr pos ci.low ci.high lod
>> c12.loc49 12 51.2 28.2 62.2 3.65
>>
>>
>> The new output I want:
>>
>> trait locus chr pos ci.low ci.high lod
>> bp c7.loc45 7 47.7 36.71 56.7 6.11
>> bp c15.loc8 15 12.0 3.96 22.8 5.29
>>
>> trait locus chr pos ci.low ci.high lod
>> hr c2.loc54 2 59.8 14.8 87.8 4.19
>> hr D15MIT184 15 22.8 12.0 36.0 3.15
>>
>> trait locus chr pos ci.low ci.high lod
>> bw c15.loc16 15 20 11 30 6.75
>>
>> heart_wt locus chr pos ci.low ci.high lod
>> trait c12.loc49 12 51.2 28.2 62.2 3.65
>>
>> I appreciate for your help for any suggestions!!
>> Joshua
>>
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