Error in 1:nrow(m): argument of length 0

[stephenturner]

I get the error Error in 1:nrow(m): argument of length 0 when trying to import either kallisto or sailfish output. Here's a reprex.

---

Load packages used here.

library(dplyr)
library(readr)
library(tximport)
library(annotables) # devtools::install_github(stephenturner/annotables)

To summarize transcripts to the gene level we'll need to use a transcript-to-gene annotation. I provide this in the annotables package (blog post; install from github with devtools::install_github("stephenturner/annotables")). The grch38_gt table contains mappings for 216133 transcripts to 65988 genes.

annotables::grch38_gt

## Source: local data frame [216,133 x 2]
## 
##            ensgene          enstxp
##              (chr)           (chr)
## 1  ENSG00000210049 ENST00000387314
## 2  ENSG00000211459 ENST00000389680
## 3  ENSG00000210077 ENST00000387342
## 4  ENSG00000210082 ENST00000387347
## 5  ENSG00000209082 ENST00000386347
## 6  ENSG00000198888 ENST00000361390
## 7  ENSG00000210100 ENST00000387365
## 8  ENSG00000210107 ENST00000387372
## 9  ENSG00000210112 ENST00000387377
## 10 ENSG00000198763 ENST00000361453
## ..             ...             ...

Download data from here: https://dl.dropboxusercontent.com/u/66281/sailfish-txps.txt to data/ directory. Take a look at what the file looks like:

readLines("data/sailfish-txps.txt", n=20)

##  [1] "# sailfish (quasi-mapping-based) v0.7.6"        
##  [2] "# [ program ] => sailfish "                     
##  [3] "# [ command ] => quant "                        
##  [4] "# [ index ] => { sailfish-grch38-index }"       
##  [5] "# [ libType ] => { IU }"                        
##  [6] "# [ threads ] => { 3 }"                         
##  [7] "# [ geneMap ] => { Homo_sapiens.GRCh38.82.gtf }"
##  [8] "# [ mates1 ] => { SRR493366_1.fastq }"          
##  [9] "# [ mates2 ] => { SRR493366_2.fastq }"          
## [10] "# [ output ] => { SRR493366-sfem }"             
## [11] "# [ mapping rate ] => { 95.2197% }"             
## [12] "# Name\tLength\tTPM\tNumReads"                  
## [13] "ENST00000415118\t8\t0\t0"                       
## [14] "ENST00000448914\t13\t0\t0"                      
## [15] "ENST00000631435\t12\t0\t0"                      
## [16] "ENST00000434970\t9\t0\t0"                       
## [17] "ENST00000632684\t12\t0\t0"                      
## [18] "ENST00000431440\t16\t0\t0"                      
## [19] "ENST00000454691\t18\t0\t0"                      
## [20] "ENST00000451044\t17\t0\t0"

Try importing:

sf <- tximport("data/sailfish-txps.txt", type="salmon", gene2tx=grch38_gt)

## Error in 1:nrow(m): argument of length 0

[stephenturner]

Also, fwiw, it's not the tbl_df that's causing an issue - tried setting to as.data.frame(grch38_gt) also. Same error.

[mikelove]

This should fix it:

1648def

it's the classic gotcha of, with a matrix with one dimension of length 1, without drop=FALSE, R converts a matrix to a vector

[mikelove]

added test: https://github.com/mikelove/tximport/blob/master/tests/testthat/test_one_sample.R