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" <chl...@mail.usask.ca>
To: "Shuhua Zhan" <sz...@uoguelph.ca>, "r-help" <r-help@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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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
