vdbR

Set of functions to help accessing microbiota database and and analyzing data

Install

Install using this command

remotes::install_github("vdblab/vdbR")

Useful functions

Connecting to the database

The database config file is a comma-delimited file as follows:

user,pass,host,dbname
me,test123,my.postgres.url.org,my_db_name

Your database config file should be placed in one of the following approved locations:

• ~/dbConfig.txt
• ~/.dbConfig.txt
• ~/.config/dbConfig.txt
• ~/.config/vdbR/dbConfig.txt

This prevents having to hardcode the path to the config file in your scripts. With your config in one of the approved locations, this connects you to the microbiome database server:

connect_database()

Database Usage

List all the available tables:

list_table_from_database(pattern="*")

Get a table from the database (loads it to your global env):

get_table_from_database("qpcr_16s_ag")
dim(qpcr_16s_ag)
# [1] 4748    7

Make a phyloseq ID based on some metadata table

test_metadata <- structure(
  list(
    sampleid = c("2133C", "1773A", "1773I", "90.tp.51", 
                 "223D", "2065C", "1773O", "1773M", "2133D", "2065D", "90.tp.97", 
                 "1773E", "2065B", "2065E", "90.tp.57", "2133G", "2065F", "1773G", 
                 "FMT.0113I", "2065G"), 
    age = c("60 and over ", 
            "60 and over ", "60 and over ", "60 and over ", "60 and over ", 
            "40-59", "60 and over ", "60 and over ", "60 and over ", "40-59", 
            "40-59", "60 and over ", "40-59", "40-59", "40-59", "60 and over ", 
            "40-59", "60 and over ", "40-59", "40-59"),
    fakemrn = c("00000001", 
                "00000002", "00000003", "00000004", "00000005", "00000001", "00000002", 
                "00000003", "00000004", "00000005", "00000001", "00000002", "00000003", 
                "00000004", "00000005", "00000001", "00000002", "00000003", "00000004", 
                "00000005")), 
  row.names = c(NA, -20L), class = "data.frame")

vdb_make_phylo(test_metadata, sampleid_col = "sampleid")

Get a dataframe of all Isabl analyses for a list of samples

sampleids <- c("2711D", "2711E", "2711F", "2711G", "2711H", "2711I", "2954A")
get_isabl_analyses(sampleids = sampleids, app_id=43)

Get QC metric for Shotgun samples

sampleids <-  c("2711D", "2711E", "2711F", "2711G", "2711H", "2711I", "2954A")
preproces_analyses <- get_isabl_analyses(sampleids = sampleids, app_id=43)
# note there are more rows than samples: one per flowcell

dplyr::tbl(psql_con, "mgx_qc") %>% 
   dplyr::filter(ia_id %in% local(preproces_analyses$ia_id)) %>% 
   dplyr::collect()

Make Shotgun Phyloseq Object

metadata <-  data.frame(identifier = sampleids)
phy <- vdb_make_phylo_mgx(metadata = metadata, sampleid_col = "identifier", app_id = 66, verbose = FALSE)
phy
phyloseq::plot_bar(phy, fill="Order")

We have currently implemented an easy way to get a phyloseq object from metaphlan results stored in the database. to do this, you need (a) some metadata about what samples you want, and (b) and Isabl application ID. Each app version gets its own ID, so specifying an application ID ensures that the results will be compatible with eachother.

For a list of apps, see

connect_database()
dplyr::tbl(psql_con, "isabl_api_application") %>% dplyr::collect()

Scripts

Development

Update docs and NAMESPACE

devtools::document()

Increment version using:

usethis::use_version()

Style package

styler::style_pkg(".")

Style tutorials

styler::style_dir("data_analysis_tutorial/", filetype = "rmd")

Auto-Name tutorial chunks

namer::name_dir_chunks("data_analysis_tutorial/")

Render Tutorials

bookdown::render_book("data_analysis_tutorial/")

Admin Tasks

These tasks aren't run by the average user, so they are not exported when loading the package. Access these functions using the ::: operator.

Add a new user

library(vdbR)
connect_database()
vdbR:::create_new_postgres_user(user_name = "nwtest", temp_pass = "test123456")

Check to see if user changed their temporary password

vdbR:::block_user_who_did_not_change_password(user_name = "nwtest", temp_pass = "test123456")

Updating database tables

TBD

History

Mirrored from Antonio Gomes's original repo at github.mskcc.org/gomesa/vdbr, and added various scripts sporadically developed over the years for database admin, processing data, and more. Moved from vdblabinternal to the Microbiome organization