[R] conditional subset and reorder dataframe rows

arun
Fri, 20 Jul 2012 20:55:24 -0000

Hi,

I guess the ' +' strand was already ordered in the "mapping"
set while '-' was not ordered.

Try this:
? test2<-mapping[with(mapping,rev(order(Chr.From))),]
?rownames(test2)<-1:nrow(test2)
?test2
????????? Probe.Set.Name Chr Chr.Strand? Chr.From Probe.X Probe.Y
1? ENSMUSG00000047459_at?? 2????????? + 155062531??? 2125??? 1008
2? ENSMUSG00000047459_at?? 2????????? + 155062326??? 1293??? 1435
3? ENSMUSG00000047459_at?? 2????????? + 155062309??? 1570??? 1082
4? ENSMUSG00000047459_at?? 2????????? + 155062305??? 2058???? 893
5? ENSMUSG00000047459_at?? 2????????? + 155062304??? 1681??? 2090
6? ENSMUSG00000047459_at?? 2????????? + 155062277???? 428??? 1484
7? ENSMUSG00000022174_at? 14????????? -? 54873546???? 388??? 2112
8? ENSMUSG00000022174_at? 14????????? -? 54873539??? 1634??? 1773
9? ENSMUSG00000022174_at? 14????????? -? 54873533??? 2141??? 1045
10 ENSMUSG00000022174_at? 14????????? -? 54873529??? 2305???? 862
11 ENSMUSG00000022174_at? 14????????? -? 54873527???? 882???? 971
12 ENSMUSG00000022174_at? 14????????? -? 54873416???? 960??? 2160


#Now I am rearranging rows

?mapping1<-mapping[c(2,3,5,1,4,6,9,10,7,8,11,12),]
test3<-mapping1[with(mapping1,rev(order(Chr.From))),]
?test3
????????? Probe.Set.Name Chr Chr.Strand? Chr.From Probe.X Probe.Y
12 ENSMUSG00000047459_at?? 2????????? + 155062531??? 2125??? 1008
11 ENSMUSG00000047459_at?? 2????????? + 155062326??? 1293??? 1435
10 ENSMUSG00000047459_at?? 2????????? + 155062309??? 1570??? 1082
9? ENSMUSG00000047459_at?? 2????????? + 155062305??? 2058???? 893
8? ENSMUSG00000047459_at?? 2????????? + 155062304??? 1681??? 2090
7? ENSMUSG00000047459_at?? 2????????? + 155062277???? 428??? 1484
1? ENSMUSG00000022174_at? 14????????? -? 54873546???? 388??? 2112
2? ENSMUSG00000022174_at? 14????????? -? 54873539??? 1634??? 1773
3? ENSMUSG00000022174_at? 14????????? -? 54873533??? 2141??? 1045
4? ENSMUSG00000022174_at? 14????????? -? 54873529??? 2305???? 862
5? ENSMUSG00000022174_at? 14????????? -? 54873527???? 882???? 971
6? ENSMUSG00000022174_at? 14????????? -? 54873416???? 960??? 2160

Not quite sure this is what you were looking for.

A.K.


----- Original Message -----
From: Iain Gallagher <iaingallagher at btopenworld.com>
To: r-help <r-help at r-project.org>
Cc:
Sent: Friday, July 20, 2012 7:40 AM
Subject: [R] conditional subset and reorder dataframe rows

Hi List

I have a dataframe (~1,200,000 rows deep) and I'd like to conditionally
reorder groups of rows in this dataframe.

I would like to reorder any rows where the Chr.Strand column contains a
'-' but reorder within subsets delineated by the Probe.Set.Name column.

# toy example ####

library(plyr)

negStrandGene <- data.frame(Probe.Set.Name =
rep('ENSMUSG00000022174_at', 6), Chr = rep(14,6), Chr.Strand =
rep('-', 6), Chr.From = c(54873546, 54873539, 54873533, 54873529,
54873527, 54873416), Probe.X = c(388,1634,2141,2305,882,960), Probe.Y = c(2112,
1773, 1045, 862, 971, 2160))

posStrandGene <- data.frame(Probe.Set.Name =
rep('ENSMUSG00000047459_at', 6), Chr = rep(2, 6), Chr.Strand =
rep('+', 6), Chr.From = c(155062277, 155062304, 155062305, 155062309,
155062326, 155062531), Probe.X = c(428, 1681, 2058, 1570, 1293, 2125), Probe.Y =
c(1484, 2090, 893, 1082, 1435, 1008))

mapping <- rbind (negStrandGene, posStrandGene)

# define a function to do what we want
revSort <- function(df){

? if (unique(df$Chr.Strand == '-'))
? return (df[order(df$Chr.From), ])
? else return (df)

}


# split the data with plyr, apply the function and recombine
test2 <- ddply(mapping, .(Probe.Set.Name), function(df) revSort(df)) # ok,
cool works

So here the rows with the '-' if Chr.Strand are reordered whilst those
with '+' are not.

My initial attempt using plyr is very inefficient and I wondered if someone
could suggest something better.

Best

Iain

??? [[alternative HTML version deleted]]


______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.