sig_testmlr_tool¶
Apply given model to predict genes using multiple linear regression.
Synopsis¶
sig_testmlr_tool
[--ds DS] [--model MODEL]
[--minval MINVAL] [--maxval MAXVAL] [--use_gctx USE_GCTX] [--xform XFORM]
Arguments¶
--help, -h
: Show this help message and exit
--help_markdown
: Print help in Markdown format
--undef_action
UNDEF_ACTION
: Action to take if an undefined argument is encountered. Default is error.
Options are {error|warn|ignore}
-o, --out
OUT
: Output path
--runtests
: Execute functional and unit tests. Default is 0
--rundemo
: Run the tool with sample inputs. Default is 0
--rpt
RPT
: Report folder prefix
--create_subdir
CREATE_SUBDIR
: Create subfolder within out for saving results. Default is 1
--verbose
VERBOSE
: Print debugging messages. Default is 1
--encode_url
ENCODE_URL
: Encode all input URLs. Default is 0
--config
CONFIG
: Argument configuration file
--ds
DS
: GCT or GCTX, Input dataset (genes x samples), minimally containing all
landmarks genes specified in the model. Non-landmark genes will be ignored
--model
MODEL
: MLR model output from SIG_TRAINMLR_TOOL to utilize to infer dependent genes
--minval
MINVAL
: Minimum value for output dataset. Lower values will be replaced with this
value. Default is 0
--maxval
MAXVAL
: Maximum value for output dataset. Greater values will be replaced with this
value. Default is 15
--use_gctx
USE_GCTX
: Outputs text GCT files if false. Default is 1
--xform
XFORM
: String. Specify any transformations to apply to data prior to training. Default
is none. Options are {none|log2|abs|pow2|zscore}
Description¶
The sig_testmlr_tool takes as input a test dataset (genes x samples) minimally containing all landmark genes and an MLR model (output by SIG_TRAINMLR_TOOL) and output inferred values for dependent genes by applying the model. Note that the values in the input dataset must match the data used for training. The standard L1000 analytical workflow employs normalized log2 transformed expression as input to the model. The --xform argument can be optionally specified to transform the input data. The output is saved as a GCTX file with the inferred dependent genes appended to the original landmark data.
Examples¶
- Apply model to landmark data.
sig_testmlr_tool --ds 'test_data.gctx' --model '/filepath/model.gctx'
- Apply model to landmark data retricting the minimum value in the output to 2.
sig_testmlr_tool --ds 'test_data.gctx' --model '/filepath/model.gctx' --minval 2