TK_LabInternship

This directory is for Lab Internship with TK Lab.

Introduction

Python Files

getCNAData.py

to get CNA data from CNA files

CNAFromCosmic

• input
  • fileName: file name which include desired CNA data
• return: CNA value with python dictionary type

Unique with gene name which is consist of first and second value of each row.

CNAonlyGene

• input
  • fileName: file name which include desired CNA data
• return: python list type include gene names with CNA

CNAwithHugo

• input
  • fileName: file name which include desired CNA data
  • review: default = True; this should be boolean; if this is True, then the function check the return value, and remove zeros
• return: python dictionary type include CNA value with gene name along HUGO type

CNAwithPatient

• input
  • fileName: file name which include desired CNA data
  • review: default = True; this should be boolean; if this is True, then the function check the return value, and remove zeros
• return: python dictionary type include CNA value with patient ID

handCNAFromCosmic

• input
  • fileName: file name which include desired CNA data from COSMIC
• return: python dictionary type; keys are a pair of (gene name, CNA value), and values are repetition number of that

onlyCNAFromCosmic

• input
  • fileName: file name which include desired CNA data
  • see: default = None; the number of column which want to see (zero base)
• return: python dictionary type which include gene name and its CNA value

The gene names are unique in return data. Nothing in columns #14 and/or #15, regard as zero.

getGeneExp.py

geneExpFromCosmic

• input
  • fileName: file name which include desired gene expression data
  • wanted: default = None; this should be None or python list type; if this is not None, then the function only select gene which is included in wanted
  • cutNormal: default = False; this should be boolean; if this is true, then the function select gene expression data only over 2 or under -2 ("over" or "under" in column #3)
  • maxlen: default = None; this should be None or integer; if this is not None, the function returns maximum maxlen number of data
• return: python dictionary type; keys are gene name, and values are python list type which contain gene expression data

geneExpInlier

• input
  • fileName: file name which include desired gene expression data
  • threshold: default = 6; this should be integer or float; the function
• return:

geneExpOnlyValue

• input
  • fileName
  • maxlen
• return

geneExpOutlier

• input
  • fileName
  • threshold
• return

getRNASeqData.py

RNASeqGeneName

• input
  • fileName
• return

RNASeqOrganName

• input
  • fileName
• return

RNASeqwithGene

• input
  • fileName
  • review
• return

RNASeqwithOrgan

• input
  • fileName
  • review
• return

selectedGene

• input
  • fileName
  • geneNum
• return

selectedGeneOrgan

• input
  • fileName
  • geneNum
  • organNum
• return

selectedOrgan

• input
  • fileName
  • organNum
• return

drawCNAData.py

Pre-requisite: getCNAData.py

This python file is