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View Code? Open in Web Editor NEWDetection of ligand-protein interactions from thermal proteome profiles (DLPTP) by FDR-controlled analysis of 2D-TPP experiments
Detection of ligand-protein interactions from thermal proteome profiles (DLPTP) by FDR-controlled analysis of 2D-TPP experiments
Dear @nkurzaw,
when I use the package function import2Dataset()
in combination with replicated measurements (each temperature * drug combination was measured twice) it crashes. The function call is
import_df <- import2dDataset(configTable = tt,
data = ll,
idVar = "ProteinID",
intensityStr = "INT_",
fcStr = "rel_fc_",
nonZeroCols = "Total Spectral Count",
geneNameVar = "Entry Name",
addCol = "Gene",
qualColName = "Total Peptides",
naStrs = c("NA")
)
The config table looks like this:
> tt
# A tibble: 20 × 14
Compound Experiment Temperature `126` `127N` `127C` `128N` `128C` `129N` `129C` `130N` `130C` `131N` RefCol
<chr> <chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 drug rep1_red 41.9 5 1 0.143 0.02 0 - - - - - 128C
2 drug rep1_red 43.6 - - - - - 5 1 0.143 0.02 0 131N
3 drug rep1_orange 45.7 5 1 0.143 0.02 0 - - - - - 128C
4 drug rep1_orange 48.7 - - - - - 5 1 0.143 0.02 0 131N
5 drug rep1_yellow 51.5 5 1 0.143 0.02 0 - - - - - 128C
6 drug rep1_yellow 54.2 - - - - - 5 1 0.143 0.02 0 131N
7 drug rep1_green 57 5 1 0.143 0.02 0 - - - - - 128C
8 drug rep1_green 59.9 - - - - - 5 1 0.143 0.02 0 131N
9 drug rep1_blue 62.1 5 1 0.143 0.02 0 - - - - - 128C
10 drug rep1_blue 64 - - - - - 5 1 0.143 0.02 0 131N
11 drug rep2_red 41.9 5 1 0.143 0.02 0 - - - - - 128C
12 drug rep2_red 43.6 - - - - - 5 1 0.143 0.02 0 131N
13 drug rep2_orange 45.7 5 1 0.143 0.02 0 - - - - - 128C
14 drug rep2_orange 48.7 - - - - - 5 1 0.143 0.02 0 131N
15 drug rep2_yellow 51.5 5 1 0.143 0.02 0 - - - - - 128C
16 drug rep2_yellow 54.2 - - - - - 5 1 0.143 0.02 0 131N
17 drug rep2_green 57 5 1 0.143 0.02 0 - - - - - 128C
18 drug rep2_green 59.9 - - - - - 5 1 0.143 0.02 0 131N
19 drug rep2_blue 62.1 5 1 0.143 0.02 0 - - - - - 128C
20 drug rep2_blue 64 - - - - - 5 1 0.143 0.02 0 131N
The data looks like:
> ll
$rep1_red
# A tibble: 6,618 × 43
Protein ProteinID `Entry Name` Gene Length Organism `Protein Description` `Protein Existence` Coverage
<chr> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl>
1 sp|A0A0B4J2D5|GAL3B_HUMAN A0A0B4J2D5 GAL3B_HUMAN GATD3B 268 Homo sa… Putative glutamine a… 5:Protein uncertain 35.4
2 sp|A0A0U1RRE5|NBDY_HUMAN A0A0U1RRE5 NBDY_HUMAN NBDY 68 Homo sa… Negative regulator o… 1:Experimental evi… 77.9
3 sp|A0AVT1|UBA6_HUMAN A0AVT1 UBA6_HUMAN UBA6 1052 Homo sa… Ubiquitin-like modif… 1:Experimental evi… 25.9
4 sp|A0JNW5|BLT3B_HUMAN A0JNW5 BLT3B_HUMAN BLTP3B 1464 Homo sa… Bridge-like lipid tr… 1:Experimental evi… 11.5
5 sp|A0MZ66|SHOT1_HUMAN A0MZ66 SHOT1_HUMAN SHTN1 631 Homo sa… Shootin-1 1:Experimental evi… 55.5
6 sp|A0PJW6|TM223_HUMAN A0PJW6 TM223_HUMAN TMEM2… 202 Homo sa… Transmembrane protei… 1:Experimental evi… 13.4
7 sp|A1A5C7|S22AN_HUMAN A1A5C7 S22AN_HUMAN SLC22… 686 Homo sa… Solute carrier famil… 1:Experimental evi… 2.48
8 sp|A1L0T0|HACL2_HUMAN A1L0T0 HACL2_HUMAN ILVBL 632 Homo sa… 2-hydroxyacyl-CoA ly… 1:Experimental evi… 12.8
9 sp|A1X283|SPD2B_HUMAN A1X283 SPD2B_HUMAN SH3PX… 911 Homo sa… SH3 and PX domain-co… 1:Experimental evi… 48.1
10 sp|A2RRP1|NBAS_HUMAN A2RRP1 NBAS_HUMAN NBAS 2371 Homo sa… NBAS subunit of NRZ … 1:Experimental evi… 3.58
# ℹ 6,608 more rows
# ℹ 34 more variables: `Protein Probability` <dbl>, `Top Peptide Probability` <dbl>, `Total Peptides` <dbl>,
# `Unique Peptides` <dbl>, `Razor Peptides` <dbl>, `Total Spectral Count` <dbl>, `Unique Spectral Count` <dbl>,
# `Razor Spectral Count` <dbl>, `Total Intensity` <dbl>, `Unique Intensity` <dbl>, `Razor Intensity` <dbl>,
# `Razor Assigned Modifications` <chr>, `Razor Observed Modifications` <lgl>, `Indistinguishable Proteins` <chr>,
# INT_126 <dbl>, INT_127N <dbl>, INT_127C <dbl>, INT_128N <dbl>, INT_128C <dbl>, INT_129N <dbl>, INT_129C <dbl>,
# INT_130N <dbl>, INT_130C <dbl>, INT_131N <dbl>, rel_fc_126 <dbl>, rel_fc_127N <dbl>, rel_fc_127C <dbl>, …
# ℹ Use `print(n = ...)` to see more rows
$rep1_orange
# A tibble: 6,545 × 43
Protein ProteinID `Entry Name` Gene Length Organism `Protein Description` `Protein Existence` Coverage
<chr> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl>
1 sp|A0A0B4J2D5|GAL3B_HUMAN A0A0B4J2D5 GAL3B_HUMAN GATD3B 268 Homo sa… Putative glutamine a… 5:Protein uncertain 28.7
2 sp|A0A0U1RRE5|NBDY_HUMAN A0A0U1RRE5 NBDY_HUMAN NBDY 68 Homo sa… Negative regulator o… 1:Experimental evi… 77.9
3 sp|A0AVT1|UBA6_HUMAN A0AVT1 UBA6_HUMAN UBA6 1052 Homo sa… Ubiquitin-like modif… 1:Experimental evi… 22.9
4 sp|A0JNW5|BLT3B_HUMAN A0JNW5 BLT3B_HUMAN BLTP3B 1464 Homo sa… Bridge-like lipid tr… 1:Experimental evi… 12.4
5 sp|A0MZ66|SHOT1_HUMAN A0MZ66 SHOT1_HUMAN SHTN1 631 Homo sa… Shootin-1 1:Experimental evi… 50.4
6 sp|A0PJW6|TM223_HUMAN A0PJW6 TM223_HUMAN TMEM2… 202 Homo sa… Transmembrane protei… 1:Experimental evi… 22.3
7 sp|A1A5C7|S22AN_HUMAN A1A5C7 S22AN_HUMAN SLC22… 686 Homo sa… Solute carrier famil… 1:Experimental evi… 2.19
8 sp|A1L0T0|HACL2_HUMAN A1L0T0 HACL2_HUMAN ILVBL 632 Homo sa… 2-hydroxyacyl-CoA ly… 1:Experimental evi… 14.1
9 sp|A1X283|SPD2B_HUMAN A1X283 SPD2B_HUMAN SH3PX… 911 Homo sa… SH3 and PX domain-co… 1:Experimental evi… 44.5
10 sp|A2RRP1|NBAS_HUMAN A2RRP1 NBAS_HUMAN NBAS 2371 Homo sa… NBAS subunit of NRZ … 1:Experimental evi… 1.14
# ℹ 6,535 more rows
# ℹ 34 more variables: `Protein Probability` <dbl>, `Top Peptide Probability` <dbl>, `Total Peptides` <dbl>,
# `Unique Peptides` <dbl>, `Razor Peptides` <dbl>, `Total Spectral Count` <dbl>, `Unique Spectral Count` <dbl>,
# `Razor Spectral Count` <dbl>, `Total Intensity` <dbl>, `Unique Intensity` <dbl>, `Razor Intensity` <dbl>,
# `Razor Assigned Modifications` <chr>, `Razor Observed Modifications` <lgl>, `Indistinguishable Proteins` <chr>,
# INT_126 <dbl>, INT_127N <dbl>, INT_127C <dbl>, INT_128N <dbl>, INT_128C <dbl>, INT_129N <dbl>, INT_129C <dbl>,
# INT_130N <dbl>, INT_130C <dbl>, INT_131N <dbl>, rel_fc_126 <dbl>, rel_fc_127N <dbl>, rel_fc_127C <dbl>, …
# ℹ Use `print(n = ...)` to see more rows
...
Importing only rep1 or rep2 works without any problem! Am I doing something wrong?
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TPP2D_1.10.0 dplyr_1.1.2 dbplyr_2.3.2 tibble_3.2.1 readr_2.1.4
loaded via a namespace (and not attached):
[1] zip_2.3.0 Rcpp_1.0.10 pillar_1.9.0 compiler_4.1.2 iterators_1.0.14 bitops_1.0-7
[7] tools_4.1.2 bit_4.0.5 lifecycle_1.0.3 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3
[13] rlang_1.1.1 openxlsx_4.2.5.2 foreach_1.5.2 DBI_1.1.3 cli_3.6.1 rstudioapi_0.14
[19] parallel_4.1.2 stringr_1.5.0 withr_2.5.0 generics_0.1.3 vctrs_0.6.2 hms_1.1.3
[25] bit64_4.0.5 grid_4.1.2 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[31] BiocParallel_1.28.3 vroom_1.6.3 limma_3.50.3 purrr_1.0.1 tidyr_1.3.0 tzdb_0.4.0
[37] ggplot2_3.4.2 magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 MASS_7.3-60 colorspace_2.1-0
[43] utf8_1.2.3 stringi_1.7.12 doParallel_1.0.17 RCurl_1.98-1.12 munsell_0.5.0 crayon_1.5.2
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