Compute deconvolution preprocessing — compute.deconvolution.preprocessing • multideconv

Give consistent names and patterns following the method_signature_cell structure to the deconvolution features

Usage

compute.deconvolution.preprocessing(deconv)

Arguments

deconv: A dataframe with the unprocessed deconvolution features

Value

A matrix of the preprocessed deconvolution features with fixed and consistent names across the different methods and signatures following the nomenclature specified in multideconv (see Readme)

Examples


data("deconvolution")

deconvolution = multideconv:::compute.deconvolution.preprocessing(deconvolution)
#> Preprocessing deconvolution features...............................................................
#> 
#> Checking consistency in deconvolution cell fractions across patients...............................................................
#> 
#> 
#> 
#> Total sum across samples of combination Quantiseq is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination Quantiseq is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> Total sum across samples of combination Epidish_BPRNACan_ is 1
#> Total sum across samples of combination Epidish_BPRNACanProMet is 1
#> Total sum across samples of combination Epidish_BPRNACan3DProMet is 1
#> Total sum across samples of combination Epidish_CBSX.HNSCC.scRNAseq is 1
#> Total sum across samples of combination Epidish_CBSX.Melanoma.scRNAseq is 1
#> Total sum across samples of combination Epidish_CBSX.NSCLC.PBMCs.scRNAseq is 1
#> 
#> Total sum across samples of combination Epidish_CCLE.TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination Epidish_CCLE.TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination Epidish_TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination Epidish_TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination Epidish_LM22 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination Epidish_LM22 is not 1:
#> 
#>  Sample_12929
#> Sample_11817
#> Sample_12935
#> Sample_13636
#> Sample_12889
#> Sample_8356
#> Sample_11522 
#> 
#> Total sum across samples of combination DeconRNASeq_BPRNACan_ is 1
#> Total sum across samples of combination DeconRNASeq_BPRNACanProMet is 1
#> Total sum across samples of combination DeconRNASeq_BPRNACan3DProMet is 1
#> Total sum across samples of combination DeconRNASeq_CBSX.HNSCC.scRNAseq is 1
#> Total sum across samples of combination DeconRNASeq_CBSX.Melanoma.scRNAseq is 1
#> Total sum across samples of combination DeconRNASeq_CBSX.NSCLC.PBMCs.scRNAseq is 1
#> 
#> Total sum across samples of combination DeconRNASeq_CCLE.TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DeconRNASeq_CCLE.TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination DeconRNASeq_TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DeconRNASeq_TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination DeconRNASeq_LM22 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DeconRNASeq_LM22 is not 1:
#> 
#>  Sample_13636 
#> 
#> Total sum across samples of combination CBSX_BPRNACan_ is 1
#> Total sum across samples of combination CBSX_BPRNACanProMet is 1
#> Total sum across samples of combination CBSX_BPRNACan3DProMet is 1
#> Total sum across samples of combination CBSX_CBSX.HNSCC.scRNAseq is 1
#> Total sum across samples of combination CBSX_CBSX.Melanoma.scRNAseq is 1
#> Total sum across samples of combination CBSX_CBSX.NSCLC.PBMCs.scRNAseq is 1
#> 
#> Total sum across samples of combination CBSX_CCLE.TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination CBSX_CCLE.TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination CBSX_TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination CBSX_TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination CBSX_LM22 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination CBSX_LM22 is not 1:
#> 
#>  Sample_12929
#> Sample_11817
#> Sample_12935
#> Sample_13636
#> Sample_8356
#> Sample_11522 
#> 
#> Total sum across samples of combination DWLS_BPRNACan_ is 1
#> Total sum across samples of combination DWLS_BPRNACanProMet is 1
#> Total sum across samples of combination DWLS_BPRNACan3DProMet is 1
#> Total sum across samples of combination DWLS_CBSX.HNSCC.scRNAseq is 1
#> Total sum across samples of combination Epidish_CBSX.Melanoma.scRNAseq is 1
#> Total sum across samples of combination DWLS_CBSX.NSCLC.PBMCs.scRNAseq is 1
#> 
#> Total sum across samples of combination DWLS_CCLE.TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DWLS_CCLE.TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination DWLS_TIL10 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DWLS_TIL10 is not 1:
#> 
#>  Sample_12929
#> Sample_15467
#> Sample_13634
#> Sample_14428
#> Sample_11817
#> Sample_14958
#> Sample_12935
#> Sample_13636
#> Sample_13774
#> Sample_14965
#> Sample_12889
#> Sample_8356
#> Sample_11918
#> Sample_11522
#> Sample_15002 
#> 
#> 
#> Total sum across samples of combination DWLS_LM22 is not 1! Remember these are proportions and the total should be 1
#> Samples which sum with combination DWLS_LM22 is not 1:
#> 
#>  Sample_12929
#> Sample_11817
#> Sample_12935
#> Sample_13636
#> Sample_12889
#> Sample_8356
#> Sample_11522 
#> Warning: 
#> Please verify your matrix