GLAD  Print-icon

Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).

GLAD File Format

This is a tab-delimited file format that contains the output results of the GLAD module. The GLAD module, a SNP analysis module, runs the R package Gain and Loss analysis of DNA (GLAD), which detects altered regions in the genomic pattern. The GLAD file format is organized as follows:

  1. The first line contains a list of labels identifying the columns.
    • Line format:
      Sample (tab) Chromosome (tab) Start.bp (tab) End.bp (tab) Num.SNPs (tab) Seg.CN
  2. The rest of the file contains one row of data for each altered chromosomal region.
    • Line format:
      (sample) (tab) (chromosome) (tab) (startPosition) (tab) (endPosition) (tab) (numberOfSNPs) (tab) (regionCN)
    • For example:
      MYNAH_p_Affy_plate_9_Mapping250K_Sty_A02_49084 (tab) 17 (tab) 41419603 (tab) 36581538 (tab) 6427 (tab) 2.06

Sample GLAD file: mynah.glad

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Updated on May 02, 2013 14:43