Loading .txt file in RforProteomics

[zillurbmb51]

Sir, I was trying to load the attached Mass spectrometry output file in Rforproteomics using openMSfile but getting this:

> ms1=openMSfile('proteinGroups_166_Bioinf.txt')
Error in .mzRBackendFromContent(x) : 
  Could not determine file type for proteinGroups_166_Bioinf.txt

Any help? I am new in this topic. Best Regards Zillur proteinGroups_166_Bioinf.txt

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] RforProteomics_1.26.0 MSnbase_2.14.2        ProtGenerics_1.20.0  
 [4] S4Vectors_0.26.1      mzR_2.22.0            Rcpp_1.0.5           
 [7] Biobase_2.48.0        BiocGenerics_0.34.0   edgeR_3.30.3         
[10] limma_3.44.3          XML_3.99-0.5         

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.4        lattice_0.20-41       digest_0.6.25        
 [4] foreach_1.5.0         mime_0.9              R6_2.4.1             
 [7] plyr_1.8.6            mzID_1.26.0           ggplot2_3.3.2        
[10] pillar_1.4.6          biocViews_1.56.2      zlibbioc_1.34.0      
[13] rlang_0.4.7           rstudioapi_0.11       R.utils_2.10.1       
[16] R.oo_1.24.0           RUnit_0.4.32          preprocessCore_1.50.0
[19] BiocParallel_1.22.0   RCurl_1.98-1.2        munsell_0.5.0        
[22] shiny_1.5.0           compiler_4.0.2        httpuv_1.5.4         
[25] pkgconfig_2.0.3       pcaMethods_1.80.0     htmltools_0.5.0      
[28] tidyselect_1.1.0      tibble_3.0.3          IRanges_2.22.2       
[31] codetools_0.2-16      crayon_1.3.4          dplyr_1.0.2          
[34] later_1.1.0.1         bitops_1.0-6          MASS_7.3-51.6        
[37] R.methodsS3_1.8.1     grid_4.0.2            RBGL_1.64.0          
[40] xtable_1.8-4          gtable_0.3.0          lifecycle_0.2.0      
[43] affy_1.66.0           magrittr_1.5          scales_1.1.1         
[46] ncdf4_1.17            graph_1.66.0          impute_1.62.0        
[49] promises_1.1.1        affyio_1.58.0         doParallel_1.0.15    
[52] ellipsis_0.3.1        generics_0.0.2        vctrs_0.3.4          
[55] iterators_1.0.12      tools_4.0.2           glue_1.4.2           
[58] purrr_0.3.4           fastmap_1.0.1         colorspace_1.4-1     
[61] BiocManager_1.30.10   vsn_3.56.0            MALDIquant_1.19.3   

[lgatto]

• openMSfile() can only be used for raw data in one of the supported formats (mzML, mzXML, ...).
• Your file contains quantitative data. Please see the MSnbase package.

[zillurbmb51]

Ok. Thank you. I was trying to use MSnbase package. > ms1=readMSData('proteinGroups_166_Bioinf.txt') Error in .mzRBackendFromContent(x) : Could not determine file type for C:\Users\zillu\OneDrive\Desktop\zillur\job_application\iphys\proteinGroups_166_Bioinf.txt

In the documentation, I did not find any option to open txt file in MSnbase. Maybe I am missing the point. Any help would be greatly appreciated. Best Regards Zillur

[lgatto]

Again, you do not have raw data and hence readMSData is not appropriate. Please, read the documentation.

[lgatto]

Start with ?readMSnSet2

[zillurbmb51]

Thank you. It helps a lot. Best Regards Zillur