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Run the TangentXY algorithm

run_tangent.Rd

Isolate tumor signal by removing systematic noise using a set of normal samples.

Usage

run_tangent(
  sif_df,
  nsig_df,
  tsig_df,
  n_latent,
  make_plots = TRUE,
  output_dir = NULL
)

Arguments

sif_df

Tibble or filepath to a text file containing sample metadata

nsig_df

Tibble or filepath to a text file containing the normal signal matrix

tsig_df

Tibble or filepath to a text file containing the tumor signal matrix

n_latent

Number of latent factors to reconstruct normal subspace

make_plots

If TRUE, generate plots of latent factor importance and effects of linear transformation

output_dir

Directory to save the plots. If NULL, the plots will be printed to the screen.

Value

A normalized tumor signal matrix

Examples

res <- run_tangent(example_sif, example_nsig_df, example_tsig_df, 5)
#> 
#> Applying linear transformation ...


#> 
#> Running SVD ...

#> 
#> Running Tangent on autosomes and chrX ...
#> Done.
#> 
#> Running Tangent on male chrY ...
#> Done.
head(res)
#>         locus tumor.female1 tumor.female2 tumor.female3 tumor.female4
#> 1     1:1-100    -1.2207454  -0.559055711  -0.299517432   -0.28416243
#> 2   1:501-600    -0.6935373   0.243068129  -0.058697541    0.33545418
#> 3 1:1001-1100    -1.2577582   0.247067958   0.007995746    0.38298884
#> 4 1:1501-1600    -0.7668358   0.069592242  -0.073116565    0.17802465
#> 5 1:2001-2100    -0.6443380   0.038542539  -0.088375329    0.18877316
#> 6 1:2501-2600    -0.8606140   0.007977117  -0.016124108   -0.02767328
#>   tumor.female5 tumor.male1 tumor.male2 tumor.male3  tumor.male4 tumor.male5
#> 1   0.113159726  0.53400373  0.22644206 -0.28089146 -0.109757605 -0.37694414
#> 2   0.169757218  0.03113847 -0.25177090  0.28867239 -0.052538095  0.26051191
#> 3  -0.057496259  0.12303867  0.31443193  0.06375461 -0.036210615  0.17367268
#> 4   0.121745948  0.05207100  0.05443208 -0.11708422 -0.104412773  0.17846010
#> 5   0.304135800  0.07381542 -0.17230641  0.42254227 -0.143297414 -0.09760822
#> 6   0.004180603 -0.03501344 -0.11574397 -0.07468204 -0.001779737  0.13265353