hbeale

read -n1 -rsp $'Press Ctrl+C to skip screen...\n'

screen -Rx

hbeale

## .screenrc 

# backspace throws an error, so fix it
bindkey -d ^? stuff ^H
bindkey -d ^@ stuff ^H

# to be able to attach to the same screen session
# from different computers without logging out:
multiuser on

hbeale

# to reproduce
# The biospecimen_analyte_combined file can be downloaded from Synapse.org under the id: `syn7499603`
library(tidyverse)
biospecimen_values=read_tsv("~/Documents/Dropbox/ucsc/operations/registry/TCGA biospecimen_analyted_combined.tsv")
biospecimen_values  %>%
mutate(
		rinNumeric=as.numeric(rinvalue),
		a260_a280_ratioNumeric=as.numeric(a260_a280_ratio),
		source=gsub("^([A-Z]*)[-_].*$", "\\1", bcr_sample_barcode)

hbeale

# definitions of calculations

# sensitivity is the ability of test to detect the disease when it is present; it is defined as # true positives/# of samples with disease or condition

# specificity is the ability of a test to exclude the disease when it is absent, it is defined as the number of true negatives/# without the disease or condition

# positive predictive value (PPV) - the likelihood that a positive test truly represents the presence of the disease or condition; it is defined as # true positives/# all positives. A test has a high PPV if a large percentage of prople who get a positive test result actually have the disease or condition.

# negative predictive value (NPV) - the likelihood that a negative test truly represents the absence of the disease or condition; it is defined as # true negatives/# all negatives. A test has a high NPV if a large percentage of prople who get a negative test result really don't have the disease or condition.

hbeale

## these are functions that I sometimes use in my code
## they are intended to be able to be run on any computer
## with R installed.

#################################
###
### load libraries
###

hbeale

for i in *.bam ; do echo -n $i; samtools view -h $i | head -1 ; done 2>&1 | grep '\['

# for malformed bams, the output is "EGAD00001001620_ICGC_MB110.sorted.bam[bam_header_read] EOF marker is
absent. The input is probably truncated."

hbeale

#################################
###
### Cautiously RENAME a comma delim list of files
###
#################################

### ASSIGN variable to input file
thisKey="Key_Renaming_26Aug2016_hb2.txt" 

### All functions require a file containing renaming information

hbeale

# File-Name:       twitter_word_cloud.R           
# Date:            2011-01-30                                
# Author:          Drew Conway
# Email:           drew.conway@nyu.edu                                      
# Purpose:         Create a comparative word cloud of two twitter hashtags
# Data Used:       
# Packages Used:   twitteR, tm, ggplot2
# Output File:     Hashtag word cloud
# Data Output:     
# Machine:         Drew Conway's MacBook Pro