diff --git a/data-raw/files-to-rda.R b/data-raw/files-to-rda.R index 0cb136e..eea5fa9 100644 --- a/data-raw/files-to-rda.R +++ b/data-raw/files-to-rda.R @@ -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() %>% @@ -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) diff --git a/data/IC_BPS.rda b/data/IC_BPS.rda new file mode 100644 index 0000000..e50524a Binary files /dev/null and b/data/IC_BPS.rda differ