Dave Tang davetang

## bam_df_to_coverage.R
#use chr22 as an example
#how many entries on the negative strand of chr22?
table(bam_df$rname == 'chr22' & bam_df$flag == 16)
# FALSE    TRUE
#3875997   24413

#function for checking negative strand
check_neg <- function(x){
  if (intToBits(x)[5] == 1){
    return(T)

## permutation_with_replacement.R
#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,repeats.allowed=T)
#      [,1]    [,2]

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

#load library
library(Rsamtools)

#read in entire BAM file
bam <- scanBam("wgEncodeRikenCageHchCellPapAlnRep1.bam")

## first.pl
#!/bin/env perl

use strict;
use warnings;

print "My very first Gist on GitHub!\n";

exit(0);

__END__
	#use chr22 as an example
	#how many entries on the negative strand of chr22?
	table(bam_df$rname == 'chr22' & bam_df$flag == 16)
	# FALSE TRUE
	#3875997 24413

	#function for checking negative strand
	check_neg <- function(x){
	if (intToBits(x)[5] == 1){
	return(T)
	#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,repeats.allowed=T)
	# [,1] [,2]
	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("Rsamtools")

	#load library
	library(Rsamtools)

	#read in entire BAM file
	bam <- scanBam("wgEncodeRikenCageHchCellPapAlnRep1.bam")
	#!/bin/env perl

	use strict;
	use warnings;

	print "My very first Gist on GitHub!\n";

	exit(0);

	__END__