@@ -8,6 +8,8 @@ export(get_clBasVec_m)

 export(get_one_hot_encoded_seqs)

 export(get_seqClLab)

 export(get_seqs_clust_list)

+export(make_dinuc_PWMs)

+export(make_sinuc_PWMs)

 export(plot_arch_for_clusters)

 export(plot_ggheatmap)

 export(plot_ggseqlogo)

@@ -1,21 +1,21 @@

-# @title Make a PWM-resembling matrix out of a given n-vector

-#

-# @description The given matrix (or simply a vector) is reshaped to have four

-# rows for four nucleotides and a relevant number of columns.

-#

-# @param mat Actually a vector that will be reshaped into a (PWM)

-# matrix of DNA sequences.

-# @param add_pseudo_counts Logical, taking values TRUE or FALSE, specifying

-# whether or not pseudocounts are added to the matrix.

-# @param scale Logical, taking values TRUE or FALSE, specifying whether or

-# not the matrix is scaled column-wise, i.e., all columns summed to 1.

-#

-# @return A (PWM) matrix with 4 rows corresponding to the 4 nucleotides (A, C,

-# G, T) and the relevant number of columns (i.e., number of elements in given

-# vector/4)

-#

-# @export

-#

+#' @title Make a PWM-resembling matrix out of a given n-vector

+#'

+#' @description The given matrix (or simply a vector) is reshaped to have four

+#' rows for four nucleotides and a relevant number of columns.

+#'

+#' @param mat Actually a vector that will be reshaped into a (PWM)

+#' matrix of DNA sequences.

+#' @param add_pseudo_counts Logical, taking values TRUE or FALSE, specifying

+#' whether or not pseudocounts are added to the matrix.

+#' @param scale Logical, taking values TRUE or FALSE, specifying whether or

+#' not the matrix is scaled column-wise, i.e., all columns summed to 1.

+#'

+#' @return A (PWM) matrix with 4 rows corresponding to the 4 nucleotides (A, C,

+#' G, T) and the relevant number of columns (i.e., number of elements in given

+#' vector/4)

+#'

+#' @export

+#'

 make_sinuc_PWMs <- function(mat, add_pseudo_counts = TRUE, scale = TRUE) {

     ##

     sinuc <- c("A", "C", "G", "T")

@@ -36,24 +36,24 @@ make_sinuc_PWMs <- function(mat, add_pseudo_counts = TRUE, scale = TRUE) {

 }

-# @title Similarly to the PWM-like matrix for mononucleotides, make one for

-#  dinucleotides

-#

-# @description This function converts the basis matrix with basis vectors

-# of dinucleotide information into matrix of dimension

-# 16 x (sequence_length) for visualization.

-#

-# @param vec Column vector of the basis matrix

-# @param add_pseudo_counts Whether pesudocounts are to be added. TRUE or FALSE.

-# @param scale Whether to perform per position scaling of the matrix. TRUE or

-# FALSE

-#

-# @return A (PWM) matrix with 16 rows corresponding to the dinucleotide

-# combinations of the four nucleotides (A, C, G, T) and the relevant number

-# of columns (i.e., number of elements in given vector/16)

-#

-# @export

-#

+#' @title Similarly to the PWM-like matrix for mononucleotides, make one for

+#'  dinucleotides

+#'

+#' @description This function converts the basis matrix with basis vectors

+#' of dinucleotide information into matrix of dimension

+#' 16 x (sequence_length) for visualization.

+#'

+#' @param vec Column vector of the basis matrix

+#' @param add_pseudo_counts Whether pesudocounts are to be added. TRUE or FALSE.

+#' @param scale Whether to perform per position scaling of the matrix. TRUE or

+#' FALSE

+#'

+#' @return A (PWM) matrix with 16 rows corresponding to the dinucleotide

+#' combinations of the four nucleotides (A, C, G, T) and the relevant number

+#' of columns (i.e., number of elements in given vector/16)

+#'

+#' @export

+#'

 make_dinuc_PWMs <- function(vec, add_pseudo_counts = TRUE, scale = TRUE) {

     # column vector is expected as input

@@ -74,6 +74,8 @@ reference:

     - collate_seqArchR_result

     - collate_clusters

     - get_seqs_clust_list

+    - make_sinuc_PWMs

+    - make_dinuc_PWMs

 articles:

new file mode 100644

@@ -0,0 +1,27 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/make_sinuc_PWMs.R

+\name{make_dinuc_PWMs}

+\alias{make_dinuc_PWMs}

+\title{Similarly to the PWM-like matrix for mononucleotides, make one for

+ dinucleotides}

+\usage{

+make_dinuc_PWMs(vec, add_pseudo_counts = TRUE, scale = TRUE)

+}

+\arguments{

+\item{vec}{Column vector of the basis matrix}

+

+\item{add_pseudo_counts}{Whether pesudocounts are to be added. TRUE or FALSE.}

+

+\item{scale}{Whether to perform per position scaling of the matrix. TRUE or

+FALSE}

+}

+\value{

+A (PWM) matrix with 16 rows corresponding to the dinucleotide

+combinations of the four nucleotides (A, C, G, T) and the relevant number

+of columns (i.e., number of elements in given vector/16)

+}

+\description{

+This function converts the basis matrix with basis vectors

+of dinucleotide information into matrix of dimension

+16 x (sequence_length) for visualization.

+}

new file mode 100644

@@ -0,0 +1,27 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/make_sinuc_PWMs.R

+\name{make_sinuc_PWMs}

+\alias{make_sinuc_PWMs}

+\title{Make a PWM-resembling matrix out of a given n-vector}

+\usage{

+make_sinuc_PWMs(mat, add_pseudo_counts = TRUE, scale = TRUE)

+}

+\arguments{

+\item{mat}{Actually a vector that will be reshaped into a (PWM)

+matrix of DNA sequences.}

+

+\item{add_pseudo_counts}{Logical, taking values TRUE or FALSE, specifying

+whether or not pseudocounts are added to the matrix.}

+

+\item{scale}{Logical, taking values TRUE or FALSE, specifying whether or

+not the matrix is scaled column-wise, i.e., all columns summed to 1.}

+}

+\value{

+A (PWM) matrix with 4 rows corresponding to the 4 nucleotides (A, C,

+G, T) and the relevant number of columns (i.e., number of elements in given

+vector/4)

+}

+\description{

+The given matrix (or simply a vector) is reshaped to have four

+rows for four nucleotides and a relevant number of columns.

+}