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mskcc
Error "replacement has 0 rows", caused by dipLogR=numeric(0)
Dear developer,
I am processing large numbers of WES samples with facets and have observed the same error in a very small number of the samples namely an R error
Error in `$<-.data.frame`(`*tmp*`, "ocn", value = numeric(0)) :
replacement has 0 rows, data has XX
where XX is any number. I investigated by running the code chunk by chunk and the error is raised at the line
out$ocn <- 2^(1 + out$cnlr.median - dipLogR)
of the internal function fitcnf0. For the problematic samples, dipLogR has value numeric(0) which R does not like at all in math operations. I traced the code back to where dipLogR is computed i.e in the function findDiploidLogR.
I include here the value of out0 before proceeding.
> out0
¦segclust num.mark nhet cnlr.median mafR
1 1 12 2 -3.011918512 NA
2 2 1356 131 -1.798816173 0.87040920
3 3 1113 129 -1.672719808 0.50768199
4 4 2591 169 -1.540583510 0.38480972
5 5 95 0 -1.449920926 NA
6 6 3549 260 -1.375430640 1.07821394
7 7 8371 617 -1.214081713 1.62760232
8 8 23391 1735 -1.153622814 1.75910412
9 9 3813 338 -1.065265524 0.38562833
10 10 9147 507 -0.986037822 1.68275186
11 11 2276 188 -0.986037822 1.00952637
12 12 590 27 -0.872059667 0.39128127
13 13 9273 668 -0.646692979 0.39995403
14 14 137519 9330 -0.497578555 0.35753481
15 15 6959 533 -0.497578555 2.91293673
16 16 111 2 -0.497578555 NA
17 17 48236 2667 -0.430391724 0.36672818
18 18 87418 5958 -0.378755987 0.35694070
19 19 1181 139 -0.305467079 0.37138545
20 20 13660 53 -0.305467079 NA
21 21 17858 1597 -0.203132374 0.36138407
22 22 60 3 -0.112683016 NA
23 23 28336 1927 -0.045396996 0.55155616
24 24 17580 1304 0.001305458 0.53605083
25 25 349 59 1.106909438 0.04739713
26 26 9 1 1.745496039 NA
Because there is no segment among the segments above with a value of mafR below 0.025, the threshold is raised to 0.05. Only line 25 of out0 satisfies this condition and therefore bsegs takes the value 25. Also, ocnlevels takes the value
> ocnlevels
[1] -3.011918512 -1.798816173 -1.672719808 -1.540583510 -1.449920926 -1.375430640 -1.214081713 -1.153622814 -1.065265524 -0.986037822
[11] -0.872059667 -0.646692979 -0.497578555 -0.430391724 -0.378755987 -0.305467079 -0.203132374 -0.112683016 -0.045396996 0.001305458
[21] 1.106909438 1.745496039
after running
levels <- unique(out0$cnlr.median)
Continuing through the function, dipLogR takes the intermediate value 1.106909438 after running
} else {
¦ ¦ # make sure bsegs is not empty
¦ ¦ if (length(bsegs) == 0) {
¦ ¦ ¦ ¦ # if no balanced segs set dipLogR at the median of cnlr
¦ ¦ ¦ ¦ dipLogR <- median(cnlr)
¦ ¦ ¦ ¦ nbal <- 0
¦ ¦ } else {
¦ ¦ ¦ ¦ dipLogR <- cnlr.median[bsegs]
¦ ¦ ¦ ¦ nbal <- num.mark[bsegs]
¦ ¦ }
}
Advancing through the code, not1plus1 takes the value FALSE and therefore we arrive at where cn2logR is computed
# find deviance for each ocnlevel
# ocn levels cannot be any lower than lr4-1
ocnlevels0 <- ocnlevels[ocnlevels > dipLogR[1]-1 & ocnlevels < dipLogR[1]]
dev1 <- sapply(ocnlevels0, facets:::dlrdev, dipLogR[1], out1)
[...]
cn2logR <- ocnlevels0[which.min(dev1)]
The problem here is that there is not a single value in the vector ocnlevels that satisfies ocnlevels > dipLogR[1]-1 & ocnlevels < dipLogR[1] which makes ocnlevels0 (and subsequently cn2logR) take the value numeric(0).
However, changing the strictly inferior in
ocnlevels[ocnlevels > dipLogR[1]-1 & ocnlevels < dipLogR[1]]
to less than or equal as follows
ocnlevels[ocnlevels > dipLogR[1]-1 & ocnlevels <= dipLogR[1]]
makes ocnlevels0 take the length-1 vector value [1] 1.106909 and subsequently cn2LogR the value 1.106909, thereby avoiding the error I described at the beginning.
Is the strictly inferior needed in ocnlevels[ocnlevels > dipLogR[1]-1 & ocnlevels < dipLogR[1]] or is it ok to replace it by a simple less than or equal to? I know that we often use interchangeably < and <= with no consequence at all but here is an example where it makes a difference.
Best, Yoann
can you share a data set that will trigger the dipLogR=numeric(0) issue you are getting?
Hello,
I am sorry I can't find again the pileup matrix that led to the error I described above. I'll make sure to keep it in case I come across this error again. I thought that the table out0 I provided to you in my previous message would be enough for you to figure out what was going on.
Best, Yoann