diff --git a/man/clean_data_matrix.Rd b/man/clean_data_matrix.Rd
new file mode 100644
index 0000000..e535404
--- /dev/null
+++ b/man/clean_data_matrix.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{clean_data_matrix}
+\alias{clean_data_matrix}
+\title{Replace NA values by zero, relocate 'sample_names' column to the very beginning and convert to a tibble}
+\usage{
+clean_data_matrix(x, sample_names)
+}
+\arguments{
+\item{x}{A dataframe}
+
+\item{sample_names}{List of sample names.}
+}
+\value{
+Cleaned tibble.
+}
+\description{
+Replace NA values by zero, relocate 'sample_names' column to the very beginning and convert to a tibble
+}
diff --git a/man/comb.Rd b/man/comb.Rd
new file mode 100644
index 0000000..2087909
--- /dev/null
+++ b/man/comb.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{comb}
+\alias{comb}
+\title{Combines the output (i.e. metadata, intensity and RT) from different clusters to one respective tibble.}
+\usage{
+comb(x, ...)
+}
+\value{
+Tibbles combining the output (metadata, intensity and RT respectively) from different clusters.
+}
+\description{
+Combines the output (i.e. metadata, intensity and RT) from different clusters to one respective tibble.
+}
diff --git a/man/compute_clusters_simple.Rd b/man/compute_clusters_simple.Rd
index 09ab9f3..3a4855b 100644
--- a/man/compute_clusters_simple.Rd
+++ b/man/compute_clusters_simple.Rd
@@ -7,7 +7,7 @@
 compute_clusters_simple(feature_tables, sample_names, mz_tol_ppm, rt_tol)
 }
 \arguments{
-\item{feature_tables}{list of tibbles List of feature tables coming from all samples.}
+\item{feature_tables}{list of tibbles feature tables coming from all samples.}
 
 \item{sample_names}{list of strings Sample names of the feature tables used to distinguish the samples.}
 
diff --git a/man/create_aligned_feature_table.Rd b/man/create_aligned_feature_table.Rd
index 034df37..66a676d 100644
--- a/man/create_aligned_feature_table.Rd
+++ b/man/create_aligned_feature_table.Rd
@@ -30,7 +30,7 @@ percentage of the m/z value. This value, multiplied by the m/z value, becomes th
 \item{cluster}{The number of CPU cores to be used}
 }
 \value{
-A tibble with three tables containing aligned metadata, intensities an RTs.
+A list of 3 tibbles containing aligned metadata, intensities an RTs.
 }
 \description{
 Align peaks from spectra into a feature table.
diff --git a/man/create_features_from_cluster.Rd b/man/create_features_from_cluster.Rd
new file mode 100644
index 0000000..84bebba
--- /dev/null
+++ b/man/create_features_from_cluster.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{create_features_from_cluster}
+\alias{create_features_from_cluster}
+\title{Group the mz and RT for particular cluster.}
+\usage{
+create_features_from_cluster(
+  features,
+  mz_tol_relative,
+  rt_tol_relative,
+  min_occurrence,
+  sample_names
+)
+}
+\arguments{
+\item{features}{The features table subsetted for a particular cluster.}
+
+\item{mz_tol_relative}{The m/z tolerance level for peak alignment.}
+
+\item{rt_tol_relative}{The retention time tolerance level for peak alignment.}
+
+\item{min_occurrence}{A minimal number of profiles a feature has to be present in.}
+
+\item{sample_names}{A list of sample names.}
+}
+\value{
+A list containing 3 tibbles: metadata, intensities and RTs.
+}
+\description{
+Group the mz and RT for particular cluster.
+}
diff --git a/man/create_intensity_row.Rd b/man/create_intensity_row.Rd
new file mode 100644
index 0000000..0976c45
--- /dev/null
+++ b/man/create_intensity_row.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{create_intensity_row}
+\alias{create_intensity_row}
+\title{Compute summed area for each sample}
+\usage{
+create_intensity_row(sample_grouped)
+}
+\arguments{
+\item{sample_grouped}{A dataframe with grouped mz and RT values for a particular cluster.}
+}
+\value{
+Summed area for each sample.
+}
+\description{
+Compute summed area for each sample
+}
diff --git a/man/create_output.Rd b/man/create_output.Rd
new file mode 100644
index 0000000..9c1223e
--- /dev/null
+++ b/man/create_output.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{create_output}
+\alias{create_output}
+\title{Create a list containing 3 tibbles: metadata, intensities and RTs.}
+\usage{
+create_output(sample_grouped, sample_names)
+}
+\arguments{
+\item{sample_grouped}{A dataframe with grouped mz and RT values for a particular cluster.}
+
+\item{sample_names}{A list of sample names.}
+}
+\value{
+A list containing 3 tibbles: metadata, intensities and RTs.
+}
+\description{
+Create a list containing 3 tibbles: metadata, intensities and RTs.
+}
diff --git a/man/create_rt_row.Rd b/man/create_rt_row.Rd
new file mode 100644
index 0000000..0059fb9
--- /dev/null
+++ b/man/create_rt_row.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{create_rt_row}
+\alias{create_rt_row}
+\title{Compute median RT for each sample}
+\usage{
+create_rt_row(sample_grouped)
+}
+\arguments{
+\item{sample_grouped}{A dataframe with grouped mz and RT values for a particular cluster.}
+}
+\value{
+Median RT for each sample.
+}
+\description{
+Compute median RT for each sample
+}
diff --git a/man/filter_based_on_density.Rd b/man/filter_based_on_density.Rd
new file mode 100644
index 0000000..fe85d5c
--- /dev/null
+++ b/man/filter_based_on_density.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{filter_based_on_density}
+\alias{filter_based_on_density}
+\title{Subset data within lower and upper bound from density estimation}
+\usage{
+filter_based_on_density(sample, turns, index, i)
+}
+\arguments{
+\item{sample}{A subset of the features_table.}
+
+\item{turns}{A list of peaks and valleys positions.}
+
+\item{index}{Whether it subsets on m/z [1] or RT [2] column.}
+
+\item{i}{Iterates over the peaks in the turns list.}
+}
+\value{
+Dataframe subsetted within lower and upper bound from density estimation.
+}
+\description{
+Subset data within lower and upper bound from density estimation
+}
diff --git a/man/find_optima.Rd b/man/find_optima.Rd
new file mode 100644
index 0000000..81e681b
--- /dev/null
+++ b/man/find_optima.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{find_optima}
+\alias{find_optima}
+\title{Compute the kernel density estimation and find the peaks and valleys of a smooth curve.}
+\usage{
+find_optima(data, bandwidth)
+}
+\arguments{
+\item{data}{A vector of m/z or RTs for a particular cluster.}
+
+\item{bandwidth}{A bandwidth value for the KDE computation.}
+}
+\value{
+A list of peaks and valleys positions.
+}
+\description{
+Compute the kernel density estimation and find the peaks and valleys of a smooth curve.
+}
diff --git a/man/remove_noise.Rd b/man/remove_noise.Rd
index debe393..e310fcd 100644
--- a/man/remove_noise.Rd
+++ b/man/remove_noise.Rd
@@ -13,7 +13,8 @@ remove_noise(
   baseline_correct_noise_percentile,
   intensity_weighted,
   do.plot,
-  cache
+  cache,
+  grouping_threshold = Inf
 )
 }
 \arguments{
@@ -40,6 +41,8 @@ run filter, to be used as the baseline threshold of signal strength.}
 \item{do.plot}{Indicates whether plot should be drawn.}
 
 \item{cache}{Whether to use cache}
+
+\item{grouping_threshold}{The maximum difference between two scans to be considered the same EIC. Default is Inf.}
 }
 \value{
 A matrix with four columns: m/z value, retention time, intensity, and group number.
diff --git a/man/validate_contents.Rd b/man/validate_contents.Rd
new file mode 100644
index 0000000..e8f9889
--- /dev/null
+++ b/man/validate_contents.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature.align.R
+\name{validate_contents}
+\alias{validate_contents}
+\title{Validates if the data is present in more than "min_occurence" of samples.}
+\usage{
+validate_contents(samples, min_occurrence)
+}
+\arguments{
+\item{samples}{A subset of the features_table.}
+
+\item{min_occurrence}{A minimal number of profiles a feature has to be present in.}
+}
+\value{
+boolean value whether it is TRUE or FALSE.
+}
+\description{
+Validates if the data is present in more than "min_occurence" of samples.
+}