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Documentation updates for latest changes

Christian Arnold authored on 20/07/2022 16:21:33
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@@ -618,7 +618,7 @@ addData <- function(GRN, counts_peaks, normalization_peaks = "DESeq_sizeFactor",
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 #' @param maxNormalizedMean_peaks Numeric or \code{NULL}. Default \code{NULL}. Maximum mean across all samples for a peak to be retained for the normalized counts table. Set to \code{NULL} for not applying the filter.
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 #' @param minNormalizedMeanRNA Numeric or \code{NULL}. Default 5. Minimum mean across all samples for a gene to be retained for the normalized counts table. Set to \code{NULL} for not applying the filter.
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 #' @param maxNormalizedMeanRNA Numeric or \code{NULL}. Default \code{NULL}. Maximum mean across all samples for a gene to be retained for the normalized counts table. Set to \code{NULL} for not applying the filter.
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-#' @param chrToKeep_peaks Character vector or \code{NULL}. Default \code{c(paste0("chr", 1:22), "chrX", "chrY")}. Vector of chromosomes that peaks are allowed to come from. This filter can be used to filter sex chromosomes from the peaks, for example.
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+#' @param chrToKeep_peaks Character vector or \code{NULL}. Default \code{NULL}. Vector of chromosomes that peaks are allowed to come from. This filter can be used to filter sex chromosomes from the peaks, for example (e.g, \code{c(paste0("chr", 1:22), "chrX", "chrY")})
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 #' @param minSize_peaks Integer or \code{NULL}. Default \code{NULL}. Minimum peak size (width, end - start) for a peak to be retained. Set to \code{NULL} for not applying the filter.
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 #' @param maxSize_peaks Integer or \code{NULL}. Default 10000. Maximum peak size (width, end - start) for a peak to be retained. Set to \code{NULL} for not applying the filter.
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 #' @param minCV_peaks Numeric or \code{NULL}. Default \code{NULL}. Minimum CV (coefficient of variation, a unitless measure of variation) for a peak to be retained. Set to \code{NULL} for not applying the filter.
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@@ -635,7 +635,7 @@ addData <- function(GRN, counts_peaks, normalization_peaks = "DESeq_sizeFactor",
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 filterData <- function (GRN, 
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                         minNormalizedMean_peaks = 5, maxNormalizedMean_peaks = NULL, 
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                         minNormalizedMeanRNA = 1,  maxNormalizedMeanRNA = NULL,
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-                        chrToKeep_peaks = c(paste0("chr", seq_len(22)), "chrX", "chrY"),
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+                        chrToKeep_peaks = NULL,
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                         minSize_peaks = NULL, maxSize_peaks = 10000,
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                         minCV_peaks = NULL, maxCV_peaks = NULL,
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                         minCV_genes = NULL, maxCV_genes = NULL,
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@@ -730,7 +730,7 @@ filterData <- function (GRN,
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   }
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   if (is.null(chrToKeep)) {
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-    chrToKeep = GRN@data$peaks$consensusPeaks %>% dplyr::pull(chr) %>% unique()
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+    chrToKeep = GRN@data$peaks$consensusPeaks %>% dplyr::pull(.data$chr) %>% unique()
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   } else {
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     futile.logger::flog.info(paste0("Filter and sort peaks and remain only those on the following chromosomes: ", paste0(chrToKeep, collapse = ",")))
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   }
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@@ -10,7 +10,7 @@ filterData(
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   maxNormalizedMean_peaks = NULL,
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   minNormalizedMeanRNA = 1,
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   maxNormalizedMeanRNA = NULL,
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-  chrToKeep_peaks = c(paste0("chr", seq_len(22)), "chrX", "chrY"),
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+  chrToKeep_peaks = NULL,
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   minSize_peaks = NULL,
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   maxSize_peaks = 10000,
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   minCV_peaks = NULL,
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@@ -31,7 +31,7 @@ filterData(
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 \item{maxNormalizedMeanRNA}{Numeric or \code{NULL}. Default \code{NULL}. Maximum mean across all samples for a gene to be retained for the normalized counts table. Set to \code{NULL} for not applying the filter.}
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-\item{chrToKeep_peaks}{Character vector. Default \code{c(paste0("chr", 1:22), "chrX", "chrY")}. Vector of chromosomes that peaks are allowed to come from. This filter can be used to filter sex chromosomes from the peaks, for example.}
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+\item{chrToKeep_peaks}{Character vector or \code{NULL}. Default \code{NULL}. Vector of chromosomes that peaks are allowed to come from. This filter can be used to filter sex chromosomes from the peaks, for example (e.g, \code{c(paste0("chr", 1:22), "chrX", "chrY")})}
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 \item{minSize_peaks}{Integer or \code{NULL}. Default \code{NULL}. Minimum peak size (width, end - start) for a peak to be retained. Set to \code{NULL} for not applying the filter.}
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@@ -36,7 +36,7 @@ performAllNetworkAnalyses(
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 \item{communities}{Numeric vector. Default \code{seq_len(10)}. Depending on what was specified in the \code{display} parameter, this parameter would indicate either the rank or the label of the communities to be plotted. i.e. for \code{communities = c(1,4)}, if \code{display = "byRank"} the results for the first and fourth largest communities will be plotted. if \code{display = "byLabel"}, the results for the communities labeled \code{"1"}, and \code{"4"} will be plotted. If set to \code{NULL}, all communities will be plotted}
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-\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will by displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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+\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will be displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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 \item{topnGenes}{Integer. Default 20. Number of genes to plot, sorted by their rank or label.}
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@@ -30,7 +30,7 @@ plotCommunitiesEnrichment(
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 \item{basenameOutput}{\code{NULL} or character. Default \code{NULL}. Basename of the output files that are produced. If set to \code{NULL}, a default basename is chosen. If a custom basename is specified, all output files will have the chosen basename as file prefix, be careful with not overwriting already existing files (if \code{forceRerun} is set to \code{TRUE})}
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-\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will by displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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+\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will be displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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 \item{communities}{\code{NULL} or numeric vector. Default \code{NULL}. If set to \code{NULL}, the default, all communities enrichments that have been calculated before are plotted. If a numeric vector is specified: Depending on what was specified in the \code{display} parameter, this parameter indicates either the rank or the label of the communities to be plotted. i.e. for \code{communities = c(1,4)}, if \code{display = "byRank"} the results for the first and fourth largest communities are plotted. if \code{display = "byLabel"}, the results for the communities labeled \code{"1"}, and \code{"4"} are plotted.}
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@@ -26,7 +26,7 @@ plotCommunitiesStats(
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 \item{basenameOutput}{\code{NULL} or character. Default \code{NULL}. Basename of the output files that are produced. If set to \code{NULL}, a default basename is chosen. If a custom basename is specified, all output files will have the chosen basename as file prefix, be careful with not overwriting already existing files (if \code{forceRerun} is set to \code{TRUE})}
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-\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will by displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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+\item{display}{Character. Default \code{"byRank"}. One of: \code{"byRank"}, \code{"byLabel"}. Specify whether the communities will be displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.}
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 \item{communities}{Numeric vector. Default \code{seq_len(10)}. Depending on what was specified in the \code{display} parameter, this parameter would indicate either the rank or the label of the communities to be plotted. i.e. for \code{communities = c(1,4)}, if \code{display = "byRank"} the results for the first and fourth largest communities will be plotted. if \code{display = "byLabel"}, the results for the communities labeled \code{"1"}, and \code{"4"} will be plotted. If set to \code{NULL}, all communities will be plotted}
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