Title: | Refitting diploid region profiles using a clustering procedure |
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Description: | This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster. |
Authors: | Andrea Poletti [aut], Gaia Mazzocchetti [aut, cre], Vincenza Solli [aut] |
Maintainer: | Gaia Mazzocchetti <[email protected]> |
License: | GPL (>= 3) |
Version: | 1.11.0 |
Built: | 2024-10-30 04:27:22 UTC |
Source: | https://github.com/bioc/BOBaFIT |
This function compute the DRrefits' input "chromosome list". It is a vector that contains the chromosomal arms considered "normal" in the cohort of samples tested (BED file), under a specific tolerance value
computeNormalChromosomes( segments, tolerance_val = 0.15, maxCN = 6, min_threshold = 1.6, max_threshold = 2.4, verbose = FALSE )
computeNormalChromosomes( segments, tolerance_val = 0.15, maxCN = 6, min_threshold = 1.6, max_threshold = 2.4, verbose = FALSE )
segments |
data.frame formatted with correct column names |
tolerance_val |
decimal value of alteration frequency. By default is 0.15 |
maxCN |
threshold of max copy number to consider. By default is 6 |
min_threshold |
minimum threshold to define a normal CN. By default is 1.60 |
max_threshold |
maximum threshold to define a normal CN. By default is 2.40 |
verbose |
print information about the processes of the function. By default is FALSE |
vector with chromosome names and plot with the alteration rate of each chromosomal arms
data("TCGA_BRCA_CN_segments") chr_list <- computeNormalChromosomes(segments = TCGA_BRCA_CN_segments)
data("TCGA_BRCA_CN_segments") chr_list <- computeNormalChromosomes(segments = TCGA_BRCA_CN_segments)
This function refits the diploid region of input copy number profiles (segments - BED file)
DRrefit( segments_chort, chrlist, maxCN = 6, clust_method = "ward.D2", verbose = FALSE )
DRrefit( segments_chort, chrlist, maxCN = 6, clust_method = "ward.D2", verbose = FALSE )
segments_chort |
data.frame formatted with correct column names |
chrlist |
list of normal chromosome arms (pathology-specific) |
maxCN |
threshold of max copy number to consider. By default is 6 |
clust_method |
clustering method. By default is "ward.D2" |
verbose |
print information about the processes of the function. By default is FALSE |
Return two data frames, one is the DRrefit-corrected segments and the other is the samples report. See the vignette for data frame descriptions.
data("TCGA_BRCA_CN_segments") chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" ) results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list)
data("TCGA_BRCA_CN_segments") chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" ) results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list)
The function plot the copy number profile before and after DRrefit recalibration
DRrefit_plot( corrected_segments, DRrefit_report, plot_viewer = F, plot_save = F, plot_format = "png", plot_path )
DRrefit_plot( corrected_segments, DRrefit_report, plot_viewer = F, plot_save = F, plot_format = "png", plot_path )
corrected_segments |
DRrefit output dataframe. |
DRrefit_report |
DRrefit output dataframe. |
plot_viewer |
Logical parameter. When it is TRUE, the function print the output plot in the R viewer.By default is FALSE. |
plot_save |
Logical parameter. When it is TRUE, the function save the plot in the chosen path and format. By default is FALSE. |
plot_format |
File format for the output plots (accepts "png", "jpg", "pdf", "tiff"). By default is "png" |
plot_path |
Path to save output plots. |
Return the sample copy number profile before and after DRrefit recalibration. The function can output the figure in the R viewer on save it in a specific path.
data("TCGA_BRCA_CN_segments") chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" ) results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list) my_segments <- results$corrected_segments my_report <- results$report DRrefit_plot(corrected_segments = my_segments, DRrefit_report = my_report, plot_viewer= FALSE, plot_save = FALSE)
data("TCGA_BRCA_CN_segments") chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" ) results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list) my_segments <- results$corrected_segments my_report <- results$report DRrefit_plot(corrected_segments = my_segments, DRrefit_report = my_report, plot_viewer= FALSE, plot_save = FALSE)
The function clusters chromosomes based on the copy number (CN) and returns a graph where it is possible to observe the different groups and two data frames (report and plot_table). See the vignette for the data frame descriptions.
PlotChrCluster( segs, clust_method = "ward.D2", plot_output = TRUE, plot_viewer = TRUE, plot_save = FALSE, plot_format = "png", plot_path, verbose = FALSE )
PlotChrCluster( segs, clust_method = "ward.D2", plot_output = TRUE, plot_viewer = TRUE, plot_save = FALSE, plot_format = "png", plot_path, verbose = FALSE )
segs |
data.frame with segments of samples. It must be formatted with correct column names (start, end, ID) |
clust_method |
clustering method. Default is "ward.D2" |
plot_output |
Whether to plot refitted profiles (logical) |
plot_viewer |
Logical parameter. When it is TRUE, the function print the output plot in the R viewer.By default is TRUE. |
plot_save |
Logical parameter. When it is TRUE, the function save the plot in the chosen path and format. By default is TRUE. |
plot_format |
File format for the output plots (accepts "png", "jpg", "pdf", "tiff"). By default is "png" |
plot_path |
Path to save output plots. |
verbose |
print information about the processes of the function. By default is FALSE |
Plot with chromosomes clustered
data(TCGA_BRCA_CN_segments) Cluster <- PlotChrCluster(segs=TCGA_BRCA_CN_segments, clust_method= "ward.D2", plot_output=FALSE)
data(TCGA_BRCA_CN_segments) Cluster <- PlotChrCluster(segs=TCGA_BRCA_CN_segments, clust_method= "ward.D2", plot_output=FALSE)
The function assign the chromosomal arm to each segment.
Popeye(segments)
Popeye(segments)
segments |
data.frame formatted with correct column names (see package vignette) |
Return a data frame containg segments with the arm annotation.
data("TCGA_BRCA_CN_segments") data <- TCGA_BRCA_CN_segments[1:9] #as it already presents the arm column data_annotated <- Popeye(segments = data)
data("TCGA_BRCA_CN_segments") data <- TCGA_BRCA_CN_segments[1:9] #as it already presents the arm column data_annotated <- Popeye(segments = data)
Segments of 100 Breast Cancer samples, downloaded from TCGA-BRCA.
TCGA_BRCA_CN_segments
TCGA_BRCA_CN_segments
A data frame with79,607 rows and 12 variables:
Chrosome which the segment belong
Starting point of the segment, in Mb
Ending point of the segment, in Mb
Width of the segment, in Mb
Strand of the segment
Sample name
Probes involved
LogR of the segments
Barcode of tCGA-BRCA database
Arm information, p o q
Chromosomal arm which the segment belong
Segments Copy Number value obtained by the logR
https://portal.gdc.cancer.gov/projects/TCGA-BRCA