Output Parser for PPCOR — ppcor • edgynode

This function parses the standard output generated by the BEELINE tool PPCOR.

ppcor(file_path)

Arguments

file_path	a file path to the PPCOR output file generated by BEELINE.

Author

Sergio Vasquez and Hajk-Georg Drost

Examples

# path to PPCOR output file
ppcor_output <- system.file('beeline_examples/PPCOR/outFile.txt', package = 'edgynode')
# import PPCOR specific output
ppcor_parsed <- ppcor(ppcor_output)
# look at output
head(ppcor_parsed)
#>              DMRT1        FGF9       RSPO1         DHH      CTNNB1        PGD2
#> DMRT1   1.00000000  0.06285391  0.05667295  0.03068397 -0.10700398  0.03588454
#> FGF9    0.06285391  1.00000000 -0.04069199  0.15500104  0.08159642  0.10065595
#> RSPO1   0.05667295 -0.04069199  1.00000000 -0.05696785  0.25643901 -0.01395769
#> DHH     0.03068397  0.15500104 -0.05696785  1.00000000  0.02933038  0.13782892
#> CTNNB1 -0.10700398  0.08159642  0.25643901  0.02933038  1.00000000 -0.00768744
#> PGD2    0.03588454  0.10065595 -0.01395769  0.13782892 -0.00768744  1.00000000
#>            WT1mKTS         SRY        DKK1        WNT4        CBX2         AMH
#> DMRT1  0.044029797  0.23407613  0.26406899 -0.09930309 -0.05091022  0.03839975
#> FGF9   0.022588525  0.06291709  0.01202886 -0.09798493 -0.09089177  0.11529006
#> RSPO1  0.046426750 -0.05942324 -0.01375457  0.26441104 -0.11552268 -0.01012561
#> DHH    0.049194278 -0.01185965  0.05381004 -0.02244906 -0.05661758  0.16616065
#> CTNNB1 0.006062759 -0.08850942 -0.01666538  0.28988015 -0.09109189  0.01892835
#> PGD2   0.013973667  0.03189519  0.02842759 -0.04388112 -0.08975747  0.15550562
#>             NR0B1       NR5A1      WT1pKTS       FOXL2         UGR        SOX9
#> DMRT1   0.0332491 -0.11899062  0.105271818 -0.02470979 -0.10318926  0.14403915
#> FGF9   -0.1029219  0.10080058 -0.056188987  0.06591005 -0.01961795  0.09115273
#> RSPO1   0.1210503 -0.21797691  0.007058986  0.10606005 -0.11521649 -0.01597226
#> DHH    -0.1037360  0.09756275 -0.012909006  0.09816339 -0.05309513  0.10482556
#> CTNNB1  0.1140244 -0.06886234 -0.100589114  0.16148999 -0.14372889  0.01416837
#> PGD2   -0.1033778  0.06797556  0.008313388  0.06296486 -0.08261076  0.09926153
#>               GATA4
#> DMRT1  -0.037706964
#> FGF9    0.033173884
#> RSPO1   0.044454388
#> DHH     0.007567477
#> CTNNB1  0.055754392
#> PGD2    0.017948991