[R] conditional subset and reorder dataframe rows
arun
smartpink111 at yahoo.com
Fri Jul 20 22:55:24 CEST 2012
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
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