Authors: Melanie Petera for original R code - Marion Landi and Melanie Petera for original Galaxy wrapper Maintainer: Melanie Petera (PFEM - INRAE - MetaboHUB)

Generic Filter

Description

Allows to remove all samples and/or variables corresponding to specific values regarding designated factors or numerical variables.

Workflow position

/repository/static/images/c22fd3a063371834/filter.png

Input files

Parameter : num + label	Format
1 : Data matrix file	tabular
2 : Sample metadata file	tabular
3 : Variable metadata file	tabular

Missing values in numerical columns of data must be coded NA if you want to use the Numerical filter on them.

Parameters

Deleting samples and/or variables according to Numerical values:: If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated

numerical parameter ("Name of the column to remove" field) equals the selected range of values (depending on the "Interval of values to remove" chosen).

To delete multiple independent intervals of value from the same parameter, it is necessary to add as many times as necessary

the corresponding column via the "Insert Identify the parameter to filter" button.

On file (only if 'yes')
Choice between sample and variable filtering (referring to the input file containing the factor).

Name of the column to filter (only if 'yes')
Column name of the numerical parameter from which we want to remove a range of values.

Interval of values to remove (only if 'yes')
Allows to choose which type of interval should be removed:
- lower: removes all values below a specified value
- upper: removes all values above a specified value
- between: removes all values both greater than a specified value and lower than another (upper) one
- extremity: removes all values that are either lower than a specified value or greater than another (upper) one

'Remove all values' + interval chosen (only if 'yes')
Numerical value(s) used as threshold, depending on the type of interval chosen above.
Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'.

Notes:
- these parameters can be used several times using the "Insert Identify the parameter to filter" button
- Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below

Deleting samples and/or variables according to Qualitative values: If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated

factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field).

To delete multiple values of the same factor, it is necessary to add as many times as necessary the corresponding factor

via the "Insert Removing a level in factor" button.

On file (only if 'yes')
Choice between sample and variable filtering (referring to the input file containing the factor).

Name of the column to filter (only if 'yes')
Column name of the factor from which we want to remove a level.

Remove factor when (only if 'yes')
Value that you want to delete from the selected column.
Each line with that value of designated factor will be deleted.

Notes:
- these parameters can be used several times using the "Insert Removing a level in factor" button
- this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value

Output files

dataMatrix: tabular output

Identical to the input Data matrix file with the sample columns and variable lines deleted according to specified filters
sampleMetadata: tabular output

Identical to the input Sample metadata file with the sample lines deleted according to specified filters
variableMetadata: tabular output

Identical to the input Variable metadata file with the variable lines deleted according to specified filters

Additional information

For more information about input files, refer to the corresponding "W4M HowTo" page:: W4M table format for Galaxy