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Documentation and citation upd
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MASHUOA committed Dec 10, 2019
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2 changes: 1 addition & 1 deletion R/Utilities.R
Original file line number Diff line number Diff line change
Expand Up @@ -678,7 +678,7 @@ cluster_image_grid<-function(clusterID,
cluster_desc<-unique(candidate$desc)[1]
}

require(reshape2)
suppressMessages(suppressWarnings(require(reshape2)))

Header_table<-NULL
Header_table$mz=candidateunique
Expand Down
47 changes: 45 additions & 2 deletions README.Rmd
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Expand Up @@ -10,6 +10,7 @@ output:
highlight: zenburn
pdf_document: default
word_document: default
bibliography: references.bib
---
-- An R package of High-resolution Informatics Toolbox for Maldi-imaging Proteomics

Expand Down Expand Up @@ -238,6 +239,50 @@ p_cluster3<-image_read(paste0(wd,"/Summary folder/cluster Ion images/5479_cluste
print(p_cluster3)
```


## References
R Packages used in this project:

+ viridisLite[@viridisLite]

+ rcdklibs[@rcdklibs]

+ rJava[@rJava]

+ data.table[@data.table]

+ RColorBrewer[@RColorBrewer]

+ magick[@magick]

+ ggplot2[@ggplot2]

+ dplyr[@dplyr]

+ stringr[@stringr]

+ protViz[@protViz]

+ cleaver[@cleaver]

+ Biostrings[@Biostrings]

+ IRanges[@IRanges]

+ Cardinal[@Cardinal]

+ tcltk[@tcltk]

+ BiocParallel[@BiocParallel]

+ spdep[@spdep1]

+ FTICRMS[@FTICRMS]

+ UniProt.ws[@UniProt.ws]



## Session information

```{r}
Expand All @@ -246,6 +291,4 @@ sessionInfo()





End of the tutorial, Enjoy~
145 changes: 115 additions & 30 deletions README.html

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85 changes: 64 additions & 21 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ output:
highlight: zenburn
pdf_document: default
word_document: default
bibliography: references.bib
---
-- An R package of High-resolution Informatics Toolbox for Maldi-imaging Proteomics

Expand Down Expand Up @@ -176,7 +177,7 @@ print(p_pmf)
## # A tibble: 1 x 7
## format width height colorspace matte filesize density
## <chr> <int> <int> <chr> <lgl> <int> <chr>
## 1 PNG 1980 1080 sRGB FALSE 17113 72x72
## 1 PNG 1980 1080 sRGB FALSE 17165 72x72
```

<img src="README_files/figure-html/unnamed-chunk-1-1.png" width="1980" />
Expand All @@ -193,12 +194,12 @@ head(peptide_pmf_result)
## # A tibble: 6 x 16
## Protein mz Peptide adduct formula isdecoy pepmz charge mz_align Score
## <int> <dbl> <fct> <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 9 1467. GGNELD~ M+H C60H96~ 0 1466. 1 1467. 0.369
## 2 9 1323. QEDQLQ~ M+H C55H88~ 0 1322. 1 1323. 0.573
## 1 9 1323. QIDQKE~ M+H C55H88~ 0 1322. 1 1323. 0.573
## 2 9 1467. GGNELD~ M+H C60H96~ 0 1466. 1 1467. 0.369
## 3 9 1469. NEEPSS~ M+H C62H94~ 0 1468. 1 1469. 3.44
## 4 9 1323. QIDQKE~ M+H C55H88~ 0 1322. 1 1323. 0.573
## 5 13 1493. MDPTDA~ M+H C62H98~ 0 1492. 1 1493. 2.43
## 6 13 1359. LKELEV~ M+H C58H10~ 0 1358. 1 1359. 0.542
## 4 9 1323. QEDQLQ~ M+H C55H88~ 0 1322. 1 1323. 0.573
## 5 13 1359. LKELEV~ M+H C58H10~ 0 1358. 1 1359. 0.542
## 6 13 1493. MDPTDA~ M+H C62H98~ 0 1492. 1 1493. 2.43
## # ... with 6 more variables: Rank <int>, Intensity <dbl>,
## # moleculeNames <fct>, Region <int>, Delta_ppm <dbl>, desc <fct>
```
Expand All @@ -213,12 +214,12 @@ head(protein_pmf_result)
## # A tibble: 6 x 9
## Protein Proscore isdecoy Intensity Score peptide_count Protein_coverage
## <int> <dbl> <int> <dbl> <dbl> <int> <dbl>
## 1 10134 0.147 0 1189179. 1.30 5 0.0978
## 2 10204 0.179 0 167823. 0.912 4 0.198
## 3 10370 0.169 0 990324. 2.06 3 0.0719
## 4 10628 0.0617 0 340804. 1.06 2 0.0553
## 5 10691 0.125 0 442322. 1.36 3 0.0861
## 6 10754 0.0699 0 93787. 2.31 1 0.0321
## 1 10003 0.0552 0 88609. 0.855 2 0.0685
## 2 1002 0.0556 0 580348. 0.843 4 0.0600
## 3 10112 0.100 0 641587. 0.889 2 0.102
## 4 10134 0.0914 0 1455153. 1.05 4 0.0745
## 5 10204 0.180 0 167823. 0.912 4 0.198
## 6 10370 0.170 0 990324. 2.06 3 0.0719
## # ... with 2 more variables: Intensity_norm <dbl>, desc <fct>
```

Expand All @@ -244,12 +245,12 @@ head(Identification_summary_table)
## # A tibble: 6 x 16
## Protein mz Peptide adduct formula isdecoy pepmz charge mz_align Score
## <int> <dbl> <fct> <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 393 1881. GMSIDQ~ M+H C81H13~ 0 1880. 1 1881. 2.56
## 2 393 1301. RPAEIY~ M+H C55H90~ 0 1300. 1 1301. 0.765
## 3 393 1170. LGALWV~ M+H C54H89~ 0 1169. 1 1170. 0.224
## 4 452 1837. DGQVIN~ M+H C74H11~ 0 1836. 1 1837. 1.72
## 5 452 932. LLEGEE~ M+H C38H66~ 0 931. 1 932. 1.78
## 6 452 2203. EMEENF~ M+H C92H14~ 0 2202. 1 2203. 0.631
## 1 148 1138. MVEFAG~ M+H C50H81~ 0 1137. 1 1138. 1.39
## 2 148 2594. AFIVWN~ M+H C121H1~ 0 2593. 1 2594. 2.31
## 3 216 1881. ITTLQQ~ M+H C77H13~ 0 1880. 1 1881. 1.64
## 4 216 1458. ELELGE~ M+H C61H10~ 0 1457. 1 1458. 0.794
## 5 393 1170. LGALWV~ M+H C54H89~ 0 1169. 1 1170. 0.224
## 6 393 1301. RPAEIY~ M+H C55H90~ 0 1300. 1 1301. 0.765
## # ... with 6 more variables: Rank <int>, Intensity <dbl>,
## # moleculeNames <fct>, Region <int>, Delta_ppm <dbl>, desc <fct>
```
Expand Down Expand Up @@ -407,6 +408,50 @@ print(p_cluster3)

<img src="README_files/figure-html/CLuster imaging-2.png" width="1980" />


## References
R Packages used in this project:

+ viridisLite[@viridisLite]

+ rcdklibs[@rcdklibs]

+ rJava[@rJava]

+ data.table[@data.table]

+ RColorBrewer[@RColorBrewer]

+ magick[@magick]

+ ggplot2[@ggplot2]

+ dplyr[@dplyr]

+ stringr[@stringr]

+ protViz[@protViz]

+ cleaver[@cleaver]

+ Biostrings[@Biostrings]

+ IRanges[@IRanges]

+ Cardinal[@Cardinal]

+ tcltk[@tcltk]

+ BiocParallel[@BiocParallel]

+ spdep[@spdep1]

+ FTICRMS[@FTICRMS]

+ UniProt.ws[@UniProt.ws]



## Session information


Expand Down Expand Up @@ -448,7 +493,7 @@ sessionInfo()
## [28] grid_3.6.1 glue_1.3.1 Biobase_2.44.0
## [31] R6_2.4.0 fansi_0.4.0 tcltk_3.6.1
## [34] XML_3.98-1.20 survival_2.44-1.1 BiocParallel_1.18.1
## [37] pacman_0.5.1 rmarkdown_1.16 purrr_0.3.2
## [37] pacman_0.5.1 rmarkdown_1.18 purrr_0.3.2
## [40] magrittr_1.5 backports_1.1.5 MASS_7.3-51.4
## [43] codetools_0.2-16 htmltools_0.4.0 BiocGenerics_0.30.0
## [46] splines_3.6.1 assertthat_0.2.1 utf8_1.1.4
Expand All @@ -457,6 +502,4 @@ sessionInfo()





End of the tutorial, Enjoy~
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11 changes: 6 additions & 5 deletions man/training_cmd.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -36,11 +36,12 @@ imaging_identification(Digestion_site="([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=
imaging_identification(Digestion_site="([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))",Fastadatabase="uniprot-Human.fasta",output_candidatelist=T,spectra_segments_per_file=4,use_previous_candidates=T,ppm=10,FDR_cutoff = 0.1,PMF_analysis=T,plot_cluster_image_grid=T,Protein_desc_of_interest=c("Histone ","GN=MBP","ACTIN"))

```{r Citations}
library(gtools)
dependencies<-gtools::getDependencies("HiTMaP", dependencies = c("Depends", "Imports", "LinkingTo"), installed=TRUE, available=TRUE, base=FALSE, recommended=FALSE)
citations<-(lapply(dependencies, citation))
#writeLines(citations,"citations.BIB")
citations
library(pacman)
p_load("gtools")
dependencies<-gtools::getDependencies("HiTMaP", dependencies = c("Depends", "Imports", "LinkingTo"), installed=TRUE, available=TRUE,
base=TRUE, recommended=FALSE)
p_load("bibtex")
write.bib(dependencies, file="references")
```

#Bovin lens FTICR
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