Prepare TF Modules 02

Create metadata table for downstream analysis

Set environment

Code

suppressMessages(suppressWarnings(source("../run_config_project_sing.R")))
show_env()

You are working on        Singularity: singularity_proj_encode_fcc 
BASE DIRECTORY (FD_BASE): /data/reddylab/Kuei 
REPO DIRECTORY (FD_REPO): /data/reddylab/Kuei/repo 
WORK DIRECTORY (FD_WORK): /data/reddylab/Kuei/work 
DATA DIRECTORY (FD_DATA): /data/reddylab/Kuei/data 

You are working with      ENCODE FCC 
PATH OF PROJECT (FD_PRJ): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC 
PROJECT RESULTS (FD_RES): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results 
PROJECT SCRIPTS (FD_EXE): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/scripts 
PROJECT DATA    (FD_DAT): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data 
PROJECT NOTE    (FD_NBK): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/notebooks 
PROJECT DOCS    (FD_DOC): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/docs 
PROJECT LOG     (FD_LOG): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/log 
PROJECT REF     (FD_REF): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/references

Set global variables

Code

TXT_FOLDER_REGION = "module_tf_shannon"

Define file labeling

Code

### set directory
txt_folder = TXT_FOLDER_REGION
txt_fdiry  = file.path(FD_RES, "region", txt_folder)
txt_fglob  = file.path(txt_fdiry, "*bed*")

### get file names
vec_txt_fpath = Sys.glob(txt_fglob)
vec_txt_fname = basename(vec_txt_fpath)

### init info table
dat = data.frame(
    "Folder" = txt_folder,
    "FName"  = vec_txt_fname,
    "FPath"  = vec_txt_fpath
)

### assign and show
dat_region_file = dat
fun_display_table(dat)

Folder	FName	FPath
module_tf_shannon	K562.hg38.TF_Module.bed.gz	/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/module_tf_shannon/K562.hg38.TF_Module.bed.gz

Code

dat = dat_region_file
dat = dat %>% 
    dplyr::mutate(
        Label = c("module_tf_shannon")
    ) %>%
    dplyr::select(Folder, FName, Label, FPath)

### assign and show
dat_region_label = dat
fun_display_table(dat)

Folder	FName	Label	FPath
module_tf_shannon	K562.hg38.TF_Module.bed.gz	module_tf_shannon	/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/module_tf_shannon/K562.hg38.TF_Module.bed.gz

Save results

Code

txt_folder = TXT_FOLDER_REGION
txt_fdiry  = file.path(FD_RES, "region", txt_folder, "summary")
txt_fname  = "metadata.label.tsv"
txt_fpath  = file.path(txt_fdiry, txt_fname)

dir.create(txt_fdiry, showWarnings = FALSE)
dat = dat_region_label
write_tsv(dat, txt_fpath)