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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