brian-bot’s gists

brian-bot / knit2synapse.R

Last active November 23, 2020 18:37

A function to allow users to leverage knitr functionality when constructing Synapse wiki content.

	#####
	## AUTHOR: BRIAN M. BOT
	## ORGANIZATION: SAGE BIONETWORKS
	##
	## ALLOW USERS TO LEVERAGE KNITR WHEN CONSTRUCTING SYNAPSE WIKI CONTENT
	#####
	## PARAMETERS:
	## file: path to a local .Rmd file which to knit
	## owner: a Synapse object which will own the resulting WikiPage (usually a Project, Folder, or File)
	## parentWikiId (optional): if the resulting WikiPage is to be a subpage of another WikiPage, this is the id for the parent WikiPage (NOTE: owner is still required)

brian-bot / synTable.R

Last active December 20, 2015 21:28

A function to render Synapse-specific markdown for table rendering

	#####
	## AUTHOR: BRIAN M. BOT
	## ORGANIZATION: SAGE BIONETWORKS
	##
	## FUNCTION TO RENDER SYNAPSE-SPECIFIC MARKDOWN FOR TABLE RENDERING
	#####
	## PARAMETERS:
	## x: an R object of class data.frame, matrix, or table
	## row.names (=TRUE): whether or not to include row names in the table (if available)
	## col.names (=TRUE): whether or not to include column names in the table (if available)

brian-bot / copyWikis.R

Last active August 29, 2015 13:58

primitive function for copying Synapse Wiki content from one resource to another

	#####
	## FUNCTION FOR COPYING ALL SYNAPSE WIKI CONTENT (AND SUBPAGES) FROM ONE OWNER RESOURCE TO ANOTHER
	## AUTHOR: BRIAN M. BOT
	#####
	## ARGUMENTS:
	## oldOwnerId - the Synapse ID of the resource (e.g. Project) to copy the wiki content from
	## newOwnerId - the Synapse ID of the resource (e.g. Project) to copy the wiki content to
	#####
	## VALUE:
	## Silently returns the Wiki headers from the new owner

brian-bot / runAttractorInCRCSC.R

Last active August 29, 2015 14:08

	runAttractorInCRCSC <- function(projectId){
	require(synapseClient)

	thisFile <- "https://gist.github.com/brian-bot/3f2b74694f58404c93fd"

	## PULL FROM THE LINK THAT WAS CREATED IN THE PROJECT AT AN EARLIER STAGE
	findLink <- synapseQuery(paste('SELECT id, name FROM link WHERE benefactorId=="', projectId, '"'))
	resolveLink <- synGet(findLink$link.id[findLink$link.name=="COAD.attractors.rnaseq.txt"][1])

	## GET THE ATTRACTOR METAGENES FOR TCGA COAD FROM THE LINK

brian-bot / nbaDraftChalk.R

Created July 20, 2016 21:08

calculation for the probability of the NBA Draft lottery going as 'chalk'

	## NBA DRAFT ODDS - CHANCES OF 'CHALK'
	chancesInOrder <- c(250, 199, 156, 119, 88, 63, 43, 28, 17, 11, 8, 7, 6, 5)

	conditionalProb <- 1
	for(i in 1:3){
	conditionalProb <- conditionalProb*chancesInOrder[i]/sum(chancesInOrder[i:length(chancesInOrder)])
	}
	conditionalProb

	# > conditionalProb

Brian M. Bot brian-bot