Progenetix File Formats

Standard Progenetix Segment Files .pgxseg

Progenetix uses a variation of a standard tab-separated columnar text file such as produced by array or sequencing CNV software, with an optional metadata header for e.g. plot or grouping instructions.

For example, with 78 samples in three NCIt cancer types, an excerpt of the segment file would look like below:

#plotpars;color_var_dup_hex=#EE4500;color_var_del_hex=#09F911
#sample_id=GSM253303;group_id=NCIT:C4028;group_label="Cervical Squamous Cell Carcinoma"
#sample_id=GSM388959;group_id=NCIT:C4024;group_label="Esophageal Squamous Cell Carcinoma"
#sample_id=GSM252886;group_id=NCIT:C6958;group_label="Astrocytic Tumor"
sample_id	reference_name	start	end	value
GSM252886	1	911484	11993973	-0.4486
GSM252886	1	12158755	22246766	0.2859
GSM252886	1	22346353	24149880	-0.5713
GSM252886	1	24160170	33603123	0.0812
GSM252886	1	33683474	37248987	-0.6478
GSM252886	1	37391587	248655165	0.0342
GSM252886	2	110819	240942225	-0.0007
GSM252886	3	119131	4655519	-0.0122
GSM252886	3	4662952	4857477	0.9273
...

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@mbaudis 2021-02-22
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