Last updated: 2017-03-07

Code version: 39c0e59

Load data

cell types: K562 GM12878 HUVEC NHLF

PCA K562

prcomp_marks(asinh(count_marks_cells.l[['K562']]), 'K562', center = T, scale = T, plot_scree = T)

PCA GM12878

prcomp_marks(asinh(count_marks_cells.l[['GM12878']]), 'GM12878', center = T, scale = T, plot_scree = T)

PCA HUVEC

prcomp_marks(asinh(count_marks_cells.l[['HUVEC']]), 'HUVEC', center = T, scale = T, plot_scree = T)

PCA NHLF

prcomp_marks(asinh(count_marks_cells.l[['NHLF']]), 'NHLF', center = T, scale = T, plot_scree = T)

PCA 4 cell types jointly

# Inverse Hyperbolic Sine Transform
data.m <- asinh(count_marks_cells.m)

# Not centered, not scaled
prcomp_marks(data.m, '4 cell types', center = F, scale = F, plot_scree = T)

# Centered, not scaled
prcomp_marks(data.m, '4 cell types', center = T, scale = F, plot_scree = T)

# Centered and scaled
prcomp_marks(data.m, '4 cell types', center = T, scale = T, plot_scree = T)

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