Source Data Underlying Manuscript Figures

Fig1aSupplementaryDataMixture.xlsx
Source data underlying Figure 1a of the manuscript. In Silico mixtures which are deconvolved.
Row names:CellType - Cell type spiked in at a particular fraction
SpikePercentage - Percentage cell type is spiked in at
TumorContent - Percentage of tumor content added to methylation mixture
CancerType - Cancer cell line used as the tumor content
Replicate - Replicate number

Cell type names ending in "_GT" are the ground truth percentages of those cell types

Rows with "cg" correspond to CpG site on 450k methylation array with the Beta values for each mixture in the columns
Fig1aSupplementaryDataDeconvolution.xlsx

Source data underlying Figure 1a of the manuscript. Results of deconvolution of in silico mixtures.
Column names:Method - Method used for deconvolution
CellType - Cell type spiked in at a particular fractionSpikePercentage - Percentage cell type is spiked in at
TumorContent - Percentage of tumor content added to methylation mixture
CancerType - Cancer cell line used as the tumor content
Replicate - Replicate number

Cell type names ending in "_GT" are the ground truth percentages of those cell types; cell type names not ending in "_GT" are the predicted cell type fractions using the specified method.
Fig1bSupplementaryDataMixture.xlsx
Source data underlying Figure 1b of the manuscript. In Vitro mixtures which are deconvolved.
Row names:Mixture - In Vitro mixture name -- this corresponds to the cell type fractions in the mixtureTumorContent - Percentage of tumor content added to methylation mixture
CancerType - Cancer cell line used as the tumor content
NoiseCoefficient - Amount of noise added to the mixture
Replicate - Replicate number
Cell type names ending in "_GT" are the ground truth percentages of those cell types

Rows with "cg" correspond to CpG site on 450k methylation array with the Beta values for each mixture in the columns
Fig1bSupplementaryDataDeconvolution.xlsx

Source data underlying Figure 1b of the manuscript. Results of deconvolution of in vitro mixtures.
Column names:Method - Method used for deconvolution
Mixture - In Vitro mixture name -- this corresponds to the cell type fractions in the mixtureTumorContent - Percentage of tumor content added to methylation mixture
CancerType - Cancer cell line used as the tumor content
NoiseCoefficient - Amount of noise added to the mixture
Replicate - Replicate number

Cell type names ending in "_GT" are the ground truth percentages of those cell types; cell type names not ending in "_GT" are the predicted cell type fractions using the specified method.
Fig1cSupplementaryDataDeconvolution.xlsx
Source data underlying Figure 1c of the manuscript. Results of deconvolution of whole blood and engineered mixtures using LTS regression and the new signature matrix.

Column names:Mixture - Mixture name -- this corresponds to the cell type fractions in the mixture
Cell type names ending in "_GT" are the ground truth percentages of those cell types; cell type names not ending in "_GT" are the predicted cell type fractions using the specified method.
RMSE1,RMSE2,R1,R2 -- these correspond to the goodness-of-fit metrics
Fig2a2bSupplementaryDataDeconvolution.xlsx
Source data underlying Figures 2a and 2b of the manuscript. Results of deconvolution of true positive and true negative samples using LTS regression and the new signature matrix.

Column names:
Sample - Sample GEO accession
RMSE1, R1, RMSE2, R2 - goodness of fit metrics which are plotted in Figures 2a and 2bCell type names - the predicted cell type fractions using LTS and the new signature
Tissue - the annotated tissue (or tissue of origin)