ShixiangWang

#!/usr/bin/env bash
# identify and remove broke images
# with imageMagick

for i in $(ls -d train/cat/* train/fish/* val/cat/* val/fish/* test/cat/* test/fish/*); do
    identify $i > /dev/null 2>&1
    if [ $? -ne 0 ]; then
      echo "file $i is broken, removing it"
      rm $i
    fi

ShixiangWang

#!/bin/bash
# function Extract for common file formats

function extract {
 if [ -z "$1" ]; then
    # display usage if no parameters given
    echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>"
 else
    if [ -f "$1" ] ; then
        NAME=${1%.*}

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ShixiangWang

#---------------------------------------------------
# Filter TCGA Replicate Samples
# Author: ShixiangWang <w_shixiang@163.com>
# ooooooo
# The filter rule following broad institute says:
#
# In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.
# 
# Analyte Replicate Filter
# The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, T analytes are dropped in preference to H and R analytes, since T is the inferior extraction protocol. If H and R are encountered, H is the chosen analyte. This is somewhat arbitrary and subject to change, since it is not clear at present whether H or R is the better protocol. If there are multiple aliquots as

ShixiangWang

library(survival)
library(survminer)

groupSurvival <- function(df, event="OS_IND", time="OS", var=NULL, time.limit=NULL, interval=c("open","close"),
                          method=c("quartile", "mean", "median", "percent", "custom"), percent=NULL, 
                          step=20, custom_fun=NULL, group1="High", group2="Low"){
    #'@param df a data.frame at leaset including three column which refer to survival info and variable used to
    #'                       set group.
    #'@param event The status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death). 
    #'For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored.

ShixiangWang

################
## 用rmd写博客 ##
################

# 作者：王诗翔
# 更新日期：2018-02-12


#>>>>>> new_rmd_post 函数 <<<<<<<<<<
# 写好模板文档后，你可以用这个函数来创建Rmarkdown文档

ShixiangWang

# Your init script
#
# Atom will evaluate this file each time a new window is opened. It is run
# after packages are loaded/activated and after the previous editor state
# has been restored.
#
# An example hack to log to the console when each text editor is saved.
#
# atom.workspace.observeTextEditors (editor) ->
#   editor.onDidSave ->

ShixiangWang

# ---------------------------
# Accessing the material
# https://tinyurl.com/bioc2017-ELMER
# ---------------------------
library("Bioc2017.TCGAbiolinks.ELMER")
Biobase::openVignette("Bioc2017.TCGAbiolinks.ELMER")

# ---------------------------
# Section 1: 
# Aims:

ShixiangWang

People

:bowtie:	😄 :smile:	😆 :laughing:
😊 :blush:	😃 :smiley:	☺️ :relaxed:
😏 :smirk:	😍 :heart_eyes:	😘 :kissing_heart:
😚 :kissing_closed_eyes:	😳 :flushed:	😌 :relieved:
😆 :satisfied:	😁 :grin:	😉 :wink:
😜 :stuck_out_tongue_winking_eye:	😝 :stuck_out_tongue_closed_eyes:	😀 :grinning:
😗 :kissing:	😙 :kissing_smiling_eyes:	😛 :stuck_out_tongue:

ShixiangWang