Prevent DEXSeq breaking transcripts entry when outputting to file
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6 weeks ago
graeme.thorn ▴ 60

I have multiple DExSeq results files I want to export to tables, but I'm finding that when I output the results directly using write.table() then with large numbers of transcripts for the exon (more than 27), the output is split over two files like:

ENSG00000005302 E052    139.860053137518    0.0139936600509854  6.47551836787261    0.0109370410611376  0.0760304762292286  chrX    11763780    1176381031  +   130 129 129 125 228 124 227 68  46  161 176 149 67  69  248 170 142 213 175 196 67  60  129 150 136 169 183 117 301 207 149 143 145 97  90  167 114 156 159 152 185 220 81  157 112 200 129 c("ENST00000649785", "ENST00000648013", "ENST00000650215", "ENST00000380692", "ENST00000649684", "ENST00000649308", "ENST00000649988", "ENST00000647701", "ENST00000650628", "ENST00000312196", "ENST00000649602", "ENST00000482871", "ENST00000649078", "ENST00000649685", "ENST00000649130", "ENST00000649649", "ENST00000398527", "ENST00000380691", "ENST00000650370", "ENST00000650050", "ENST00000473380", "ENST00000649797", "ENST00000648918", "ENST00000380693", "ENST00000468149", "ENST00000648614", "ENST00000361672",
"ENST00000648207", "ENST00000337339", "ENST00000649851", "ENST00000649271", "ENST00000648889", "ENST00000494268", "ENST00000421368", "ENST00000647869", "ENST00000647985", "ENST00000647857")

I have looked directly at the output result for this line, and the row-break is in the output:

> dxr1[2765,]

LRT p-value: full vs reduced

DataFrame with 1 row and 10 columns
                             groupID   featureID     exonBaseMean
                         <character> <character>        <numeric>
ENSG00000005302:E052 ENSG00000005302        E052 139.860053137518
                             dispersion             stat             pvalue
                              <numeric>        <numeric>          <numeric>
ENSG00000005302:E052 0.0139936600509854 6.47551836787261 0.0109370410611376
                                   padj              genomicData
                              <numeric>                <GRanges>
ENSG00000005302:E052 0.0760304762292286 chrX:11763780-11763810:+
                           countData
                            <matrix>
ENSG00000005302:E052 130:129:129:...
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            transcripts
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 <list>
ENSG00000005302:E052 c("ENST00000649785", "ENST00000648013", "ENST00000650215", "ENST00000380692", "ENST00000649684", "ENST00000649308", "ENST00000649988", "ENST00000647701", "ENST00000650628", "ENST00000312196", "ENST00000649602", "ENST00000482871", "ENST00000649078", "ENST00000649685", "ENST00000649130", "ENST00000649649", "ENST00000398527", "ENST00000380691", "ENST00000650370", "ENST00000650050", "ENST00000473380", "ENST00000649797", "ENST00000648918", "ENST00000380693", "ENST00000468149", "ENST00000648614", "ENST00000361672", \n"ENST00000648207", "ENST00000337339", "ENST00000649851", "ENST00000649271", "ENST00000648889", "ENST00000494268", "ENST00000421368", "ENST00000647869", "ENST00000647985", "ENST00000647857")

but doesn't show when looking at the entry directly:

> dxr1[2765,"transcripts"]
[[1]]
 [1] "ENST00000649785" "ENST00000648013" "ENST00000650215" "ENST00000380692"
 [5] "ENST00000649684" "ENST00000649308" "ENST00000649988" "ENST00000647701"
 [9] "ENST00000650628" "ENST00000312196" "ENST00000649602" "ENST00000482871"
[13] "ENST00000649078" "ENST00000649685" "ENST00000649130" "ENST00000649649"
[17] "ENST00000398527" "ENST00000380691" "ENST00000650370" "ENST00000650050"
[21] "ENST00000473380" "ENST00000649797" "ENST00000648918" "ENST00000380693"
[25] "ENST00000468149" "ENST00000648614" "ENST00000361672" "ENST00000648207"
[29] "ENST00000337339" "ENST00000649851" "ENST00000649271" "ENST00000648889"
[33] "ENST00000494268" "ENST00000421368" "ENST00000647869" "ENST00000647985"
[37] "ENST00000647857"

Is there a way to prevent this occurring?

I could use sed after the fact to join the lines together, but would prefer an R solution.

R DExSeq • 189 views
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How are you using write.table, could you share the code?

Maybe use paste before writing to a file?

# example
x <- list(paste0("ENST", seq(1, 10^8, 10^7)))
x
# [[1]]
#  [1] "ENST1"        "ENST10000001" "ENST20000001"
#  [4] "ENST30000001" "ENST40000001" "ENST50000001"
#  [7] "ENST60000001" "ENST70000001" "ENST80000001"
# [10] "ENST90000001"

write(paste(unlist(x), collapse = " "), "temp.txt")

# temp.txt
#ENST1 ENST10000001 ENST20000001 ENST30000001 ENST40000001 ENST50000001 ENST60000001 ENST70000001 ENST80000001 ENST90000001
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