layer_fixedMotif: Custom 2-D convolution wrapper for fixed IGMs or PWMs

Description Usage Arguments Value Author(s)

Description

Custom 2-D convolution wrapper for fixed motifs, such as those coming from a database.

Usage

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layer_fixedMotif(object, filters, motif_maxlen, fixed.motifs,
  fixed.offsets, input_shape = NULL, strides = c(1L, 1L),
  padding = "valid", activation = "sigmoid", use_bias = TRUE,
  name = "fixedMotif_conv", trainable = FALSE)

Arguments

object

Keras model object.

filters

Number of convolutional filters.

motif_maxlen

Maximum length of the motifs.

fixed.motifs

List of motifs to be used as filters.

fixed.offsets

Vector of offset values.

input_shape

Dimensionality of the input (integer) not including the samples axis. This argument is required when using this layer as the first layer in a model.

strides

An integer or list of 2 integers, specifying the strides of the convolution along the width and height. Can be a single integer to specify the same value for all spatial dimensions. Specifying any stride value != 1 is incompatible with specifying any dilation_rate value != 1.

padding

one of "valid" (default) or "same" (case-insensitive).

activation

Activation function to use. Default is the sigmoid activation.

use_bias

Boolean, whether the layer uses a bias vector. Default is to include a bias.

name

An optional name string for the layer. Should be unique in a model (do not reuse the same name twice). It will be autogenerated if it isn't provided. Default is 'fixedMotif_conv'.

trainable

Whether the layer weights will be updated during training. Default is FALSE.

Value

A Keras model with the added layer.

Author(s)

Matthew Ploenzke, ploenzke@g.harvard.edu


mPloenzke/learnMotifs documentation built on May 27, 2019, 11:55 a.m.