Dave Tang davetang

🦀

Just a dude trying to learn computational stuff and disseminating said stuff onto the interweb.

davetang / transfac_to_tess.pl

Last active December 24, 2015 12:09

Convert the TRANSFAC matrix into a matrix readable by TESS (Transcription Element Search System).

davetang / random_forest.R

Last active December 23, 2015 01:49

From two sets of dinucleotide counts, use random forests to create a predictor

	#install if necessary
	install.packages("randomForest")

	#load library
	library(randomForest)

	#I have two sets of dinucleotide counts stored in
	#my_random_loci_seq_di and my_refseq_tss_seq_di

	head(my_refseq_tss_seq_di,2)

davetang / intersect_coordinate.R

Last active May 1, 2018 18:43

Given two list of coordinates, find the ones that overlap/intersect

	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("GenomicRanges")

	#load library
	library(GenomicRanges)

	#create a GRanges object given an object, my_refseq_loci
	head(my_refseq_loci,2)
	# refseq_mrna chromosome_name transcript_start transcript_end strand

davetang / get_sequence.R

Last active March 23, 2017 15:23

From a data frame with chromosomal coordinates, obtain the sequence, and calculate the dinucleotide frequencies

	#I want to fetch sequences from
	#my_random_loci and my_refseq_tss
	head(my_random_loci,2)
	chr start end strand
	1 chr18 59415403 59415407 +
	2 chr22 8535632 8535636 -

	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("BSgenome.Hsapiens.UCSC.hg19")

davetang / biomart_refseq.R

Last active May 12, 2022 06:55

Using biomaRt to fetch all human mRNA refSeqs and their corresponding chromosome coordinates

	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("biomaRt")

	#load library
	library("biomaRt")

	#use ensembl mart
	ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")

davetang / random_region.R

Last active April 17, 2018 20:56

Sampling random regions of the hg19 genome and obtaining the corresponding sequence

	#how many regions to sample?
	number <- 50000

	#how many bp to add to start
	span <- 4

	#some necessary packages
	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("BSgenome")

davetang / cmd_line_param.R

Last active December 22, 2015 17:28

An example R script that takes in 2 command line parameters, checks whether these 2 arguments are digits and then sums them.

	#!/bin/env Rscript

	#usage
	usage <- 'Usage: cmd_line_param.R <integer_1> <integer_2>';

	#store command line arguments
	args <- commandArgs(trailingOnly = T)

	#conditional checks
	if (length(args) != 2){

davetang / comb_with_replacement.R

Created September 9, 2013 02:43

Calculate the number of combinations with replacement

	comb_with_replacement <- function(n, r){
	return( factorial(n + r - 1) / (factorial(r) * factorial(n - 1)) )
	}

	#have 3 elements, choosing 3
	comb_with_replacement(3,3)
	#[1] 10

davetang / perm_without_replacement.R

Created September 8, 2013 15:20

Function for calculating number of permutations without replacement

	perm_without_replacement <- function(n, r){
	return(factorial(n)/factorial(n - r))
	}

	#16 choices, choose 16
	perm_without_replacement(16,16)
	#[1] 2.092279e+13

	#16 choices, choose 3
	perm_without_replacement(16,3)

davetang / permutation_without_replacement.R

Created September 8, 2013 14:28

Calculating the number of permutations without repetition/replacement

	#install if necessary
	install.packages('gtools')
	#load library
	library(gtools)
	#urn with 3 balls
	x <- c('red', 'blue', 'black')
	#pick 2 balls from the urn with replacement
	#get all permutations
	permutations(n=3,r=2,v=x)
	# [,1] [,2]