Question

What I am trying to select the rows that have the same gene_id, but have the minimum value of the start coordinates: href_pos$start. Why do I get this error, even though I have a memory limit of ~ 16Gb? Or what am I doing wrong? I have the following code:

head(href_pos, 5)

    chr      region    start      end strand nu   gene_id
1  chr1 start_codon 67000042 67000044      +  . NM_032291
2  chr1         CDS 67000042 67000051      +  0 NM_032291
3  chr1        exon 66999825 67000051      +  . NM_032291
4  chr1         CDS 67091530 67091593      +  2 NM_032291
5  chr1        exon 67091530 67091593      +  . NM_032291

d1 <- ddply(as.data.frame(href_pos), “gene_id”, function(href_pos) href_pos[which.min(href_pos$start), ])
Error: cannot allocate vector of size 283 Kb
In addition: Warning messages:
1: In lapply(dfs, function(df) levels(df[[var]])) :
Reached total allocation of 16383Mb: see help(memory.size)

Answer 1

Proof that your syntax is fine:

#Create a minimal, reproducible example
gene_id <- gl(3, 3, 9, labels <- letters[1:3])
start <- rep(1:3, 3)
href_pos <- data.frame(gene_id=gene_id, start=start)

d1 <- ddply(as.data.frame(href_pos), "gene_id", function(href_pos) href_pos[which.min(href_pos$start), ])
 gene_id  start
1      a      1
2      b      1
3      c      1

To do it with data.table as Chase suggests, this should work:

require(data.table)
HREF_POS <- data.table(href_pos)
setkey(HREF_POS, gene_id)
MINS <- HREF_POS[HREF_POS[,start] %in% HREF_POS[ ,min(start), by=gene_id]$V1,]