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Transmart Loader

操作指南

  1. 下载/创建临床数据, 将 数据文件 与 map文件 放到服务器上某个路径.
  2. 修改并保存 clinical.params. (*.params的定义在 参数列表 部分说明)
  3. 导入临床数据
./load_clinical.sh clinical.params
  1. 检查 gpl 是否已经存在于 tranSMART
./check_gpl.sh
  • 如果gpl已存在于列表, 跳过下面三个步骤
  1. (可选) 从transmart dataset 下载注释数据
  2. (可选) 修改并保存 annoataion.params .
  3. (可选) 导入注释
./load_annotation.sh annotation.params
  1. 修改并保存 expression.params .
  2. 导入分子表达数据
./load_expression.sh expression.params

Done!

执行脚本

  • load_clinial.sh
  • load_expression.sh
  • load_annotation.sh
  • chk_gpl.sh

参数文件

  • clinical.params
  • expression.params
  • annotation.params

参数列表

clinical.params

# data  
DATA_LOCATION="/home/transmart/datasets/RanchoGSE4698/clinical"  
COLUMN_MAP_FILE="Acute_Lymphoblastic_Leukemia_Kirschner_Schwabe_GSE4698_Mapping_File.txt"  

# info  
STUDY_ID="GSE4698"  
TOP_NODE="\\Public Studies\\Acute Lymphoblastic Leukemia_Kirschner_Schwabe_GSE4698"  

# security  
SECURITY_REQUIRED="N"  

# not using  
WORD_MAP_FILE=x  
RECORD_EXCLUSION_FILE=x
Field Name Meaning
DATA_LOCATION 数据文件夹路径.
COLUMN_MAP_FILE map文件名.
STUDY_ID Study id.
TOP_NODE Top node.
(TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
SECURITY_REQUIRED 是否保密?
WORD_MAP_FILE Word map file.
RECORD_EXCLUSION_FILE Record exclusion file.

expression.params

# data
DATA_LOCATION="/home/transmart/datasets/RanchoGSE4698/expression"
DATA_FILE_PREFIX="Acute_Lymphoblastic_Leukemia_Kirschner_Schwabe_GSE4698_Gene_Expression_Data"
MAP_FILENAME=\
"Acute_Lymphoblastic_Leukemia_"\
"Kirschner_Schwabe_GSE4698_"\
"Subject_Sample_Mapping_File.txt"\

# info
STUDY_ID="GSE4698"
TOP_NODE="\\Public Studies\\Acute Lymphoblastic Leukemia_Kirschner_Schwabe_GSE4698"
SOURCE_CD=""

# security
SECURITY_REQUIRED="N"
Field Name Meaning
DATA_LOCATION 分子表达量数据文件夹.
DATA_FILE_PREFIX 数据文件的前缀.
MAP_FILENAME Map 文件名.
STUDY_ID Study id.
TOP_NODE Top node.
(TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
SOURCE_CD 需要包含的SOURCE_CD.
与map文件中的_SOURCE_CD_ 字段相关.
默认值: STD
SECURITY_REQUIRED 是否保密?

annotation.params

# data
DATA_LOCATION="/home/transmart/datasets/EtriksGSE43696/annotation"
SOURCE_FILENAME="GPL6480.txt"

# info
ANNOTATION_TITLE="Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name Version)"
GPL_ID="GPL6480"

# col numbers
PROBE_COL=2
GENE_SYMBOL_COL=3
GENE_ID_COL=4
ORGANISM_COL=5

# header?
SKIP_ROWS=0
Field Name Meaning
DATA_LOCATION 注释数据文件夹路径.
SOURCE_FILENAME 数据文件名.
ANNOTATION_TITLE 注释标题. (从下载压缩包的params文件复制)
GPL_ID GPL id.
PROBE_COL Column index of the probe ID.
GENE_SYMBOL_COL Column index of the gene symbol.
GENE_ID_COL Column index of the gene ID.
ORGANISM_COL Column index of the organism.
SKIP_ROWS Number of rows to skip.
Note: This script does not assume a header row is present.
If a header row exists, this should be set to one.

UI Explain

  • TOP_NODE_PREFIX
    top node prefix
  • STUDY_NAME
    study name
  • TOP_NODE (TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
    top node
  • CATEGORY_CD
    category cd