MPI for parallel computing is avaliable under R 4.0.0 for linux and Mac OS platforms.
Gene expression data of normal tissues (Lung, Prostate and Thyroid) from the GTEx study are included.
Rename DeMixT_S1 function to DeMixT_DE.
Disabled OpenMP under R 4.0.0 for Mac OS platform.
Added pi01 and pi02 as input values for users to initialize the proportion estimation.
Added nspikein as an input value in the DeMixT, DeMixT_S1 and DeMixT_GS functions to specify how many spike-in normal reference samples need to be generated; Setting nspikein at null as a default value, the number of spike-in normal reference samples equal the min(200, 0.3 x My), where My is the number of mixed samples; By setting nspikein equals 0, no spike-in normal reference will be generated; If the input value of data.N2 is not null, nspikein will be forced to be 0.
Added DeMixT_GS function, new proposed gene selection method which applies profile likelihood, for proportion estimation.
Added simulate_2comp function for users to simulate test data for 2-component de-convolution.
Added simulate_3comp function for users to simulate test data for 3-component de-convolution.
Added row names and column names for all output values.
Added gene.selection.method as an input value for DeMixT function. The default is 'GS'.
Added ngene.Profile.selected as an input value for DeMixT function. The default is NA.
New package DeMixT, for cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms