Filter CMap metadata
filterCMapMetadata(
metadata,
cellLine = NULL,
timepoint = NULL,
dosage = NULL,
perturbationType = NULL
)Data frame (CMap metadata) or character (respective filepath)
Character: cell line (if NULL, all values are loaded)
Character: timepoint (if NULL, all values are loaded)
Character: dosage (if NULL, all values are loaded)
Character: type of perturbation (if NULL, all
perturbation types are loaded)
Filtered CMap metadata
Other functions related with the ranking of CMap perturbations:
as.table.referenceComparison(),
getCMapConditions(),
getCMapPerturbationTypes(),
loadCMapData(),
loadCMapZscores(),
parseCMapID(),
plot.perturbationChanges(),
plot.referenceComparison(),
plotTargetingDrugsVSsimilarPerturbations(),
prepareCMapPerturbations(),
print.similarPerturbations(),
rankSimilarPerturbations()
cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")
#> cmapMetadata.txt not found: downloading data...
#> Extracting cmapMetadata.txt.gz...
#> Loading CMap metadata from cmapMetadata.txt...
filterCMapMetadata(cmapMetadata, cellLine="HEPG2", timepoint="2 h",
dosage="25 ng/mL")
#> sig_id pert_id pert_iname pert_type cell_id pert_dose
#> <char> <char> <char> <char> <char> <num>
#> 1: CYT001_HEPG2_2H:CSH1:25 CSH1 CSH1 trt_lig HEPG2 25
#> 2: CYT001_HEPG2_2H:CTF1:25 CTF1 CTF1 trt_lig HEPG2 25
#> 3: CYT001_HEPG2_2H:CXCL6:25 CXCL6 CXCL6 trt_lig HEPG2 25
#> 4: CYT001_HEPG2_2H:EFNA4:25 EFNA4 EFNA4 trt_lig HEPG2 25
#> 5: CYT001_HEPG2_2H:EFNA5:25 EFNA5 EFNA5 trt_lig HEPG2 25
#> 6: CYT001_HEPG2_2H:EPHA3:25 EPHA3 EPHA3 trt_lig HEPG2 25
#> 7: CYT001_HEPG2_2H:FGF1:25 FGF1 FGF1 trt_lig HEPG2 25
#> 8: CYT001_HEPG2_2H:FGF2:25 FGF2 FGF2 trt_lig HEPG2 25
#> 9: CYT001_HEPG2_2H:FGF6:25 FGF6 FGF6 trt_lig HEPG2 25
#> 10: CYT001_HEPG2_2H:FGF9:25 FGF9 FGF9 trt_lig HEPG2 25
#> 11: CYT001_HEPG2_2H:FLT3LG:25 FLT3LG FLT3LG trt_lig HEPG2 25
#> 12: CYT001_HEPG2_2H:GDNF:25 GDNF GDNF trt_lig HEPG2 25
#> 13: CYT001_HEPG2_2H:GIP:25 GIP GIP trt_lig HEPG2 25
#> 14: CYT001_HEPG2_2H:HBEGF:25 HBEGF HBEGF trt_lig HEPG2 25
#> 15: CYT001_HEPG2_2H:IL13:25 IL13 IL13 trt_lig HEPG2 25
#> 16: CYT001_HEPG2_2H:IL15:25 IL15 IL15 trt_lig HEPG2 25
#> 17: CYT001_HEPG2_2H:IL21:25 IL21 IL21 trt_lig HEPG2 25
#> 18: CYT001_HEPG2_2H:IL22:25 IL22 IL22 trt_lig HEPG2 25
#> 19: CYT001_HEPG2_2H:IL24:25 IL24 IL24 trt_lig HEPG2 25
#> 20: CYT001_HEPG2_2H:IL28A:25 IL28A IL28A trt_lig HEPG2 25
#> 21: CYT001_HEPG2_2H:IL29:25 IL29 IL29 trt_lig HEPG2 25
#> 22: CYT001_HEPG2_2H:IL31:25 IL31 IL31 trt_lig HEPG2 25
#> 23: CYT001_HEPG2_2H:IL4:25 IL4 IL4 trt_lig HEPG2 25
#> 24: CYT001_HEPG2_2H:IL6:25 IL6 IL6 trt_lig HEPG2 25
#> 25: CYT001_HEPG2_2H:IL7:25 IL7 IL7 trt_lig HEPG2 25
#> 26: CYT001_HEPG2_2H:IL9:25 IL9 IL9 trt_lig HEPG2 25
#> 27: CYT001_HEPG2_2H:NTF3:25 NTF3 NTF3 trt_lig HEPG2 25
#> 28: CYT001_HEPG2_2H:TNF:25 TNF TNF trt_lig HEPG2 25
#> 29: CYT001_HEPG2_2H:TNFSF11:25 TNFSF11 TNFSF11 trt_lig HEPG2 25
#> 30: CYT001_HEPG2_2H:TNFSF12:25 TNFSF12 TNFSF12 trt_lig HEPG2 25
#> 31: CYT001_HEPG2_2H:TNFSF13:25 TNFSF13 TNFSF13 trt_lig HEPG2 25
#> sig_id pert_id pert_iname pert_type cell_id pert_dose
#> pert_dose_unit pert_idose pert_time pert_time_unit pert_itime
#> <char> <char> <int> <char> <char>
#> 1: ng/mL 25 ng/mL 2 h 2 h
#> 2: ng/mL 25 ng/mL 2 h 2 h
#> 3: ng/mL 25 ng/mL 2 h 2 h
#> 4: ng/mL 25 ng/mL 2 h 2 h
#> 5: ng/mL 25 ng/mL 2 h 2 h
#> 6: ng/mL 25 ng/mL 2 h 2 h
#> 7: ng/mL 25 ng/mL 2 h 2 h
#> 8: ng/mL 25 ng/mL 2 h 2 h
#> 9: ng/mL 25 ng/mL 2 h 2 h
#> 10: ng/mL 25 ng/mL 2 h 2 h
#> 11: ng/mL 25 ng/mL 2 h 2 h
#> 12: ng/mL 25 ng/mL 2 h 2 h
#> 13: ng/mL 25 ng/mL 2 h 2 h
#> 14: ng/mL 25 ng/mL 2 h 2 h
#> 15: ng/mL 25 ng/mL 2 h 2 h
#> 16: ng/mL 25 ng/mL 2 h 2 h
#> 17: ng/mL 25 ng/mL 2 h 2 h
#> 18: ng/mL 25 ng/mL 2 h 2 h
#> 19: ng/mL 25 ng/mL 2 h 2 h
#> 20: ng/mL 25 ng/mL 2 h 2 h
#> 21: ng/mL 25 ng/mL 2 h 2 h
#> 22: ng/mL 25 ng/mL 2 h 2 h
#> 23: ng/mL 25 ng/mL 2 h 2 h
#> 24: ng/mL 25 ng/mL 2 h 2 h
#> 25: ng/mL 25 ng/mL 2 h 2 h
#> 26: ng/mL 25 ng/mL 2 h 2 h
#> 27: ng/mL 25 ng/mL 2 h 2 h
#> 28: ng/mL 25 ng/mL 2 h 2 h
#> 29: ng/mL 25 ng/mL 2 h 2 h
#> 30: ng/mL 25 ng/mL 2 h 2 h
#> 31: ng/mL 25 ng/mL 2 h 2 h
#> pert_dose_unit pert_idose pert_time pert_time_unit pert_itime
#> distil_id
#> <char>
#> 1: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:I06|CYT001_HEPG2_2H_X2_B12:I06|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:I06
#> 2: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:I08|CYT001_HEPG2_2H_X2_B12:I08|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:I08
#> 3: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:K02|CYT001_HEPG2_2H_X2_B12:K02|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:K02
#> 4: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F02|CYT001_HEPG2_2H_X2_B12:F02|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F02
#> 5: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F04|CYT001_HEPG2_2H_X2_B12:F04|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F04
#> 6: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:K10|CYT001_HEPG2_2H_X2_B12:K10|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:K10
#> 7: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:K18|CYT001_HEPG2_2H_X2_B12:K18|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:K18
#> 8: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F12|CYT001_HEPG2_2H_X2_B12:F12|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F12
#> 9: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:M08|CYT001_HEPG2_2H_X2_B12:M08|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:M08
#> 10: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:M12|CYT001_HEPG2_2H_X2_B12:M12|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:M12
#> 11: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:M14|CYT001_HEPG2_2H_X2_B12:M14|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:M14
#> 12: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:O12|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:O12
#> 13: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:H12|CYT001_HEPG2_2H_X2_B12:H12|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:H12
#> 14: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:H18|CYT001_HEPG2_2H_X2_B12:H18|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:H18
#> 15: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:B19|CYT001_HEPG2_2H_X2_B12:B19|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:B19
#> 16: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:B21|CYT001_HEPG2_2H_X2_B12:B21|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:B21
#> 17: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:H11|CYT001_HEPG2_2H_X2_B12:H11|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:H11
#> 18: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:D15|CYT001_HEPG2_2H_X2_B12:D15|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:D15
#> 19: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:D17|CYT001_HEPG2_2H_X2_B12:D17|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:D17
#> 20: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:D19|CYT001_HEPG2_2H_X2_B12:D19|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:D19
#> 21: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:D21|CYT001_HEPG2_2H_X2_B12:D21|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:D21
#> 22: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:D23|CYT001_HEPG2_2H_X2_B12:D23|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:D23
#> 23: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F03|CYT001_HEPG2_2H_X2_B12:F03|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F03
#> 24: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F07|CYT001_HEPG2_2H_X2_B12:F07|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F07
#> 25: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F09|CYT001_HEPG2_2H_X2_B12:F09|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F09
#> 26: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:F13|CYT001_HEPG2_2H_X2_B12:F13|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:F13
#> 27: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:H17|CYT001_HEPG2_2H_X2_B12:H17|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:H17
#> 28: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:L09|CYT001_HEPG2_2H_X2_B12:L09|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:L09
#> 29: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:L23|CYT001_HEPG2_2H_X2_B12:L23|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:L23
#> 30: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:N03|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:N03
#> 31: CYT001_HEPG2_2H_X1_B7_DUO52HI53LO:N05|CYT001_HEPG2_2H_X2_B12:N05|CYT001_HEPG2_2H_X3_B7_DUO52HI53LO:N05
#> distil_id