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export IC_BPS.rda aka MS_1.rda #5

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export IC_BPS.rda aka MS_1.rda #5

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24 changes: 15 additions & 9 deletions data-raw/files-to-rda.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,16 +24,17 @@ hg19_chr_list <- read.table(hg19_path, col.names = c("chr", "end")) %>%
filter(chr %in% paste0("chr", seq(1, 21)))
usethis::use_data(hg19_chr_list)

#### MS_1.rda ####
# MS_1.rda includeS feature_meta, sample_meta, ic_bps, ic_bps_sig, ic_bps_stat, ic_bps_stat_sig
# not sure if there is a way to export a rda containing multiple data.frame
#### IC_BPS.rda ####
# IC_BPS.rda includes ic_bps, ic_bps_sig, ic_bps_stat, ic_bps_stat_sig, feature_meta, sample_meta
# in the forms of a list
url1 <- "https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-022-12197-2/MediaObjects/41598_2022_12197_MOESM1_ESM.xlsx"

GET(url1, httr::write_disk(tf <- tempfile(fileext = ".xlsx")))
httr::GET(url1, httr::write_disk(tf <- tempfile(fileext = ".xlsx")))
fh <- readxl::read_excel(tf, sheet = 3L, col_names = FALSE)
feature_meta <- fh[-1,1:8] %>%
janitor::row_to_names(row_number = 1) %>%
janitor::clean_names()
janitor::clean_names() %>%
as.data.frame()
sample_meta <- fh[c(1,2),-c(1:8)] %>%
t() %>%
as.data.frame() %>%
Expand All @@ -46,14 +47,19 @@ ic_bps <- fh[-1, c(1, 9:ncol(fh))] %>%
column_to_rownames(., "Peptide sequence") %>%
mutate(across(everything(), as.numeric))
ic_bps_stat <- readxl::read_excel(tf, sheet = 4L, col_names = TRUE) %>%
rename("peptide_sequence" = "Peptide sequence")
rename("peptide_sequence" = "Peptide sequence") %>%
as.data.frame()
ic_bps_stat_sig <- readxl::read_excel(tf, sheet = 5L, col_names = TRUE) %>%
rename("peptide_sequence" = "Peptide sequence") %>%
rename("accession" = "Accession")
rename("accession" = "Accession") %>%
as.data.frame()
ic_bps_sig <- ic_bps %>%
rownames_to_column(., "peptide_sequence") %>%
filter(peptide_sequence %in% ic_bps_stat_sig$peptide_sequence) %>%
dplyr::filter(peptide_sequence %in% ic_bps_stat_sig$peptide_sequence) %>%
column_to_rownames(., "peptide_sequence")


IC_BPS = list(ic_bps, ic_bps_sig, ic_bps_stat, ic_bps_stat_sig, feature_meta, sample_meta)
names(IC_BPS) = c("ic_bps", "ic_bps_sig", "ic_bps_stat", "ic_bps_stat_sig",
"feature_meta", "sample_meta")
usethis::use_data(IC_BPS)

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