In UW-GAC/contactparser: Parse the TOPMed contact table

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contactparser

The contactparser package was designed to parse and reformat the Contacts table on the TOPMed website.

Installation

You can install the released version of contactparser from github with:

# install.packages("devtools") 
devtools::install_github("UW-GAC/contactparser")

Example

This package has one primary function to read, parse, and reformat the contacts table. It starts with either a csv file or an html file, parses it, and reshapes the table so that it can easily be filtered by TOPMed study, project, or contact type (PI, Co-PI, Contact, etc.).

First, export the table to a csv file with the "export" button. Then call:

library(contactparser)
csv_file <- system.file(package = "contactparser", "testdata", "example.csv")
parsed <- parse_contact_table(csv_file)
parsed

You can also save the webpage as an html file and parse the contact table from the html:

library(contactparser)
html_file <- system.file(package = "contactparser", "testdata", "example.html")
parsed <- parse_contact_table(html_file)
parsed

Once you've parsed the file, you can easily filter to specific types of contacts using dplyr functions:

library(dplyr, quietly = TRUE)

# Just PIs:
pis <- parsed %>%
  filter(contact_type %in% c("pi", "co_pi"))
pis

There are two functions you can use to create a string of emails that you can cut and paste into your email client. In both cases, the list is sorted by default, and emails for duplicate records only appear once.

You can use get_emails to returns a string that you can use to email PIs:

email_string <- get_emails(pis)
email_string

Alternately, you can use print_emails to print the same string as a message:

print_emails(pis)

UW-GAC/contactparser documentation built on Feb. 5, 2020, 4:59 a.m.