Command Line Interface

RAPDOR

usage: RAPDOR <command> [<args>]

Sub-commands

Analyze

Runs the main RAPDOR Tool

RAPDOR Analyze [-h] --input INPUT [--sep SEP] --design-matrix DESIGN_MATRIX
               [--logbase LOGBASE] [--distance-method DISTANCE_METHOD]
               [--kernel-size KERNEL_SIZE] [--method METHOD] [--eps EPS]
               [--permutations PERMUTATIONS] --output OUTPUT
               [--global-permutation] [--json JSON]
               [--num-threads NUM_THREADS]

Named Arguments

--input

Path to the csv file containing protein counts as well as any additional information

--sep

Seperator of the csv files (must be the same for the data and experimental design)

Default: `` ``

--design-matrix

Design matrix specifying which columns in the –input contain the count data

--logbase

If input counts are log transformed please set the log base via this flag

--distance-method

Distance Method to use for calculation of sample differences. Can be one of [‘Jensen-Shannon-Distance’, ‘KL-Divergence’, ‘Euclidean-Distance’]

Default: 'Jensen-Shannon-Distance'

--kernel-size

Uses an averaging kernel to run over fractions. This usually o stabilizes between sample variance. Set to 0 to disable this

Default: 3

--method

Method used for p-value calculation. One of ANOSIM or PERMANOVA. Default is None and will skip p-Value calculation

--eps

Epsilon added to counts. This is useful if kl-divergence is used for distance calculations since it willresult in nan for zero counts

Default: 0

--permutations

Number of permutations used for ANOSIM or PERMANOVA.

Default: 999

--output

Output table file to store results

--global-permutation

Will use all proteins as background in ANOSIM or PERMANOVA p-value calculation. This might be unreliable

Default: False

--json

Will write an output json file

--num-threads

Number of cores used for permutation analysis. Per default uses all cores

Default: 4

Dash

Runs the RAPDOR GUI

RAPDOR Dash [-h] [--input INPUT] [--sep SEP] [--design-matrix DESIGN_MATRIX]
            [--logbase LOGBASE] [--port PORT] [--host HOST] [--debug]

Named Arguments

--input

Path to the csv file containing protein counts as well as any additional information

--sep

Seperator of the csv files (must be the same for the data and experimental design)

Default: `` ``

--design-matrix

Design matrix specifying which columns in the –input contain the count data

--logbase

If input counts are log transformed please set the log base via this flag

--port

Port to run the Dash server (Default: 8080)

Default: '8080'

--host

Host IP used by the dash server to serve the application (Default:127.0.0.1)

Default: '127.0.0.1'

--debug

Runs dashboard in debug mode

Default: False