getBlockAverageMatrixFromBreakpoints {CNVScope} | R Documentation |

This function produces several matrix outputs of averages and areas of matrix blocks, given a pair of vectors for breakpoints.

`whole_matrix` |
the large, whole matrix from which blocks are taken |

`breakpoints_col` |
An integer list of column breakpoints, including 1 and the number of columns in the whole matrix. |

`breakpoints_row` |
An integer list of row breakpoints, including 1 and the number of rows in the whole matrix. |

`outputs` |
A list of the following possible outputs (default all): "blockaverages_reformatted_by_index","blockaverages_reformatted_by_label","blockaverages_matrix_idx_area","blockaverages_matrix_idx_avg","blockaverages_matrix_label_avg", or "blockaverages_matrix_label_area" |

An output list of the following:

blockaverages_reformatted_by_index a matrix of the block averages and areas, in long format, with indexes used to generate the averages.

blockaverages_reformatted_by_label a matrix of the block averages and areas, in long format, with labels of the indexes used to generate the averages.

blockaverages_matrix_idx_area a matrix of the block areas, with indexes based on the original row/col index used to generate the data.

blockaverages_matrix_idx_avg a matrix of the block averages, with indexes based on the original row/col index used to generate the data.

blockaverages_matrix_label_area a matrix of the block areas, with indexes based on the original row/col label used to generate the data.

blockaverages_matrix_label_avg a matrix of the block averages, with indexes based on the original row/col label used to generate the data.

load(system.file("extdata","nbl_result_matrix_sign_small.rda",package = "CNVScope")) set.seed(303) mat<-matrix(data=runif(n = 25),nrow=5,ncol=5,dimnames = list(c("chr1_0_5000", "chr1_5000_10000","chr1_10000_15000","chr1_15000_20000","chr1_20000_25000"), c("chr1_0_5000","chr1_5000_10000","chr1_10000_15000","chr1_15000_20000","chr1_20000_25000"))) breakpoints_col<-c(1,2,4,5) breakpoints_row<-c(1,2,4,5) foreach::registerDoSEQ() getBlockAverageMatrixFromBreakpoints(whole_matrix=mat,breakpoints_col=breakpoints_col, breakpoints_row=breakpoints_row) ## Not run: #extra examples mat<-matrix(data=round(runif(min = 0,max=100,n = 25)),nrow=5,ncol=5, dimnames = list(c("chr1_0_5000","chr1_5000_10000","chr1_10000_15000","chr1_15000_20000", "chr1_20000_25000"),c("chr2_0_50000","chr2_50000_100000", "chr2_100000_150000","chr2_150000_200000","chr2_200000_250000"))) breakpoints_col<-c(1,2,4,5) breakpoints_row<-c(1,2,4,5) avg_results<-getBlockAverageMatrixFromBreakpoints(whole_matrix=mat, breakpoints_col=breakpoints_col,breakpoints_row=breakpoints_row) avg_results$blockaverages_reformatted_by_label avg_results$blockaverages_reformatted_by_index whole_matrix=mat mat<-matrix(data=round(runif(min = 0,max=100,n = 25)),nrow=5,ncol=5, dimnames = list(c("chr1_0_5000","chr1_5000_10000","chr1_10000_15000", "chr1_15000_20000","chr1_20000_25000"),c("chr2_0_50000", "chr2_50000_100000","chr2_100000_150000", "chr2_150000_200000","chr2_200000_250000"))) breakpoints_col<-c(1,2,4,5) breakpoints_row<-c(1,2,4,5) avg_results<-getBlockAverageMatrixFromBreakpoints(whole_matrix=mat, breakpoints_col=breakpoints_col,breakpoints_row=breakpoints_row) avg_results$blockaverages_reformatted_by_label avg_results$blockaverages_reformatted_by_index whole_matrix=mat submatrix<-nbl_result_matrix_sign_small breakpoints_row_jointseg<-jointseg::jointSeg(submatrix,K=5)$bestBkp breakpoints_col_jointseg<-jointseg::jointSeg(t(submatrix),K=5)$bestBkp submatrix_avg_results<-getBlockAverageMatrixFromBreakpoints(whole_matrix=submatrix, breakpoints_col=breakpoints_col_jointseg,breakpoints_row=breakpoints_row_jointseg) ## End(Not run)

[Package *CNVScope* version 3.6.0 Index]