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sig_annotate_tool

Read or modify metadata for a dataset

Synopsis

sig_annotate_tool [--ds DS] [--row_meta ROW_META] [--column_meta COLUMN_META] [--strip_matrix STRIP_MATRIX]

Arguments

--ds DS : Dataset in GCT or GCTX format

--row_meta ROW_META : Row annotations as a TSV file. The first column or a column named id should match the row ids in the dataset

--column_meta COLUMN_META : Column annotations as a TSV file. The first column or a column named id should match the column ids in the dataset

--strip_matrix STRIP_MATRIX : If selected will output the original matrix with the specified annotations removed.. Default is none. Options are {row|column|both|none}

Description

This tool extracts annotations of rows and columns from a dataset.

Example

  • Extract row and column annotations from a dataset

sig_annotate_tool --ds 'data.gctx'

  • Update row and column annotations

sig_annotate_tool --ds 'data.gctx' --row_meta 'row_meta.tsv' --column_meta 'column_meta.tsv'

  • Remove matrix column annotations

sig_annotate_tool --ds 'data.gctx' --strip_matrix 'column'