devtools_history.R

In thierrycnam/igfuns: Analyzes of Ig sequencing data

usethis::use_build_ignore("devtools_history.R")
usethis::use_build_ignore("data-raw/")
usethis::use_package("shiny")
usethis::use_package("dplyr")
usethis::use_package("kableExtra")
usethis::use_package("ggplot2")
usethis::use_package("ggpubr")
usethis::use_package("rlang")
usethis::use_package("RSQLite")
usethis::use_package("data.table")
usethis::use_package("parallel")
usethis::use_package("RColorBrewer")
usethis::use_package("tibble")
usethis::use_package("forcats")
usethis::use_package("purrr")
usethis::use_package("magrittr")
usethis::use_package("ggsci")
usethis::use_package("circlize")
# bregs <- read.csv("~/Data/Cyril/BRegs/bregs.csv")
# save(bregs,
#      file = "~/R/src/My_Packages/igfuns/data/bregs.RData")
# bregs$v <- factor(paste0("VH-", substr(bregs$vh, 1, 1)))
# bregs$j <- factor(paste0("JH-", substr(bregs$jh, 1, 1)))
# bregs$length_v <- sapply(paste0(bregs$fr1, bregs$cdr1, bregs$fr2, bregs$cdr2, bregs$fr3, bregs$cdr3, bregs$fr4), nchar)

## Single Cell LB
sql_query <-
'SELECT hc.*
FROM heavy_chains hc
JOIN mutations_hc muts
ON muts.name = hc.name
WHERE hc.evalue <= 10e-3
AND hc.vh != ""
AND hc.jh != ""
AND hc.fr1 != ""
AND hc.cdr1 != ""
AND hc.fr2 != ""
AND hc.cdr2 != ""
AND hc.fr3 != ""
AND hc.stop = 0
AND hc.wgxg = 1
AND hc.inframe = 1
AND hc.alnstart <= 9
AND fr4 != "";'
list_files_sc_lb <- list.files(path = "~/Desktop/", patter="*.db", full.names = TRUE)
dim(mc_get_data_frame(list_files_sc_lb, sql_query))
# save(sc_lb, file="data/sc_lb.rda")

a <- list()
for (i in list_files_sc_lb) {
  print(i);
  a[[i]] <- get_df_from_sqlite(input_filename = i, sql_query = sql_query)
}
sc_lb <- do.call(rbind, a)
save(sc_lb, file="data/sc_lb.rda")