Output Parser for PIDC — pidc • edgynode

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

pidc(file_path)

Arguments

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

Author

Sergio Vasquez and Hajk-Georg Drost

Examples

# path to PIDC output file
pidc_output <- system.file('beeline_examples/PIDC/outFile.txt', package = 'edgynode')
# import PIDC specific output
pidc_parsed <- pidc(pidc_output)
#> Repairing names...
#> New names:
#> * `` -> ...1
#> * `` -> ...2
#> * `` -> ...3
#> * `` -> ...4
#> * `` -> ...5
#> * ...
# look at output
head(pidc_parsed)
#>               UGR   WT1mKTS     GATA4   WT1pKTS     FOXL2     DMRT1      DKK1
#> UGR            NA 1.6981356 1.7419339 0.9328237 0.5833557 0.5394874 0.4875994
#> WT1mKTS 1.6981356        NA 1.9492986 1.7285506 0.4257225 0.3675658 0.4222820
#> GATA4   1.7419339 1.9492986        NA 1.5211502 0.3248479 0.2710701 0.5039969
#> WT1pKTS 0.9328237 1.7285506 1.5211502        NA 1.9380037 1.1064496 1.1142675
#> FOXL2   0.5833557 0.4257225 0.3248479 1.9380037        NA 1.0208649 0.9988726
#> DMRT1   0.5394874 0.3675658 0.2710701 1.1064496 1.0208649        NA 1.9335954
#>             RSPO1    CTNNB1      WNT4     NR0B1       SRY     NR5A1       DHH
#> UGR     1.0550622 0.9081777 0.8541194 1.3069457 0.8014759 0.8717131 0.2615545
#> WT1mKTS 0.4302253 0.3610701 0.4703146 0.9112473 0.3459958 1.2281750 0.1499480
#> GATA4   0.6075879 0.5885704 0.7093712 1.1209276 0.3217279 1.2313751 0.2234883
#> WT1pKTS 1.6302553 1.7376486 0.9965633 0.9123949 1.6907037 1.8385828 0.3444927
#> FOXL2   1.7825687 1.8449245 1.4937821 1.2336704 1.5203266 1.8513456 0.4433224
#> DMRT1   0.4809264 1.3579193 0.9141091 0.1685123 1.8693122 0.2032254 1.4674785
#>               PGD2        AMH      FGF9      SOX9      CBX2
#> UGR     0.19641000 0.25821112 0.2141864 0.2722022 1.9952165
#> WT1mKTS 0.45683241 0.08391267 0.1036291 0.3939993 1.6591269
#> GATA4   0.07440499 0.13321898 0.1181354 0.2289278 1.5500483
#> WT1pKTS 0.34194065 0.42162686 0.3886432 0.7100558 0.9478118
#> FOXL2   0.49867316 0.49069906 0.4985856 0.6425182 1.0763603
#> DMRT1   1.46334430 1.46118868 1.4877271 1.7196495 0.6571565