create_extData_excel.rmd

---
title: "R Notebook"
author: paulbuckley
date: 22/12/2021
output: html_document
---

```{r}
library(data.table)
library(xlsx)
library(dplyr)
```

## Read files into R

```{r}

SHEET1_COV2=fread(file="/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/1_COV2_MODEL_IMMSCORES.csv")
SHEET2_GBM= fread(file="/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/2_GBM_MODEL_IMMSCORES.csv")
SHEET3=fread(file="/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/3_TESLA_MODEL_IMMSCORES.csv")
SHEET4 = fread("../../../2019_11_26-RuiTestedPeptidesCollatedData/2019_11_26-collected_tested153peptides_stats_updatedNov19.tsv")

SHEET4=SHEET4  %>% dplyr::rename(
  Peptide=Mut_peptide,HLA_Allele=HLA_allele,Immunogenicity=tcell_response_updatedNov19) %>% mutate(
    Immunogenicity = ifelse(Immunogenicity=='positive','Positive','Negative'))

```

# write to XLSX

```{r}

# Write the first data set in a new workbook
write.xlsx(SHEET1_COV2, file = "/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/BenchmarkingExtendedData.xlsx",
      sheetName = "SARS-COV-2-BENCHMARKING", append = FALSE)

write.xlsx(SHEET4, file = "/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/BenchmarkingExtendedData.xlsx",
           sheetName="GBM_FULL_DATASET", append=TRUE)

# Add a second data set in a new worksheet
write.xlsx(SHEET2_GBM, file = "/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/BenchmarkingExtendedData.xlsx",
           sheetName="GBM_BENCHMARKING", append=TRUE)
# Add a third data set
write.xlsx(SHEET3, file = "/Users/paulbuckley/Dropbox/ImmunogenicityBenchmark_V2_EmergingViruses/ImmunogenicityBenchmark_V2_EmergingViruses_BIB_RR/Supp_Files/BenchmarkingExtendedData.xlsx",
           sheetName="TESLADATA_BENCHMARKING", append=TRUE)



```