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sig_getgenesets_tool

Extract top and botton N genes from dataset

Synopsis:

sig_getgenesets_tool [--ds DS] [--set_size SET_SIZE] [--cid CID] [--rid RID] [--row_space ROW_SPACE] [--sort_order SORT_ORDER] [--es_tail ES_TAIL] [--id_field ID_FIELD] [--desc_field DESC_FIELD] [--suffix SUFFIX] [--dim DIM] [--enforce_set_size ENFORCE_SET_SIZE] [--min_set_size MIN_SET_SIZE]

Arguments

--ds DS : Input dataset

--set_size SET_SIZE : Integer, size of each geneset. Default is 50

--cid CID : List of column ids to extract as a GRP file or cell array.

--rid RID : List of row ids to extract as a GRP file or cell array

--row_space ROW_SPACE : Common row-id spaces to extract. Use '_probeset' if affy_ids present.. Default is custom. Options are {lm|lm_probeset|bing|bing_probeset|full|custom}

--sort_order SORT_ORDER : String, sort order of gene expression. Default is descend. Options are {descend|ascend}

--es_tail ES_TAIL : String, specifies which tail to return.. Default is both. Options are {both|up|down}

--id_field ID_FIELD : String, specifies an alternate metadata field to use for selecting features instead of ids.. Default is _id

--desc_field DESC_FIELD : String, specifies a metadata field to use for the output desc field.

--suffix SUFFIX : String, Append string to each set name.

--dim DIM : String, Dimension of matrix to operate on.. Default is column. Options are {column|row}

--enforce_set_size ENFORCE_SET_SIZE : Boolean, Assert if set sizes match N exactly. A set size of less than N can result in cases where an alternate id_field is specified and there are duplicate entries. Set to false to disable this constraint.. Default is 1

--min_set_size MIN_SET_SIZE : Integer, minimum set size. Sets with fewer members are excluded from the ouput.. Default is 0

Description

Returns the top and bottom N genesets for the score dataset DS sorted according to --sort_order. SORTORDER can be 'descend' or 'ascend'. UP and DN are structures with length equal to the number of columns in DS. Supports subsetting to specified row_space before extracting genesets with --row_space option.

Outputs a GMT file.

Each row in the structure has the the following fields: hd : String header, same as the column id in DS with either '_UP' or '_DN' appended. desc : String descriptor. Set to ''. entry : Cell array of N row identifiers in DS.

Examples

  • Get top and bottom 50 genes of each column in given dataset

sig_getgenesets_tool --ds 'raw_data.gctx' --set_size 50

  • Get top and bottom 50 landmark genes of each column in given gene id dataset

sig_getgenesets_tool --ds 'raw_data.gctx' --set_size 50 --row_space lm

  • Get top and bottom 50 landmark genes of each column in given affy id dataset

sig_getgenesets_tool --ds 'raw_data.gctx' --set_size 50 --row_space lm_probeset