Coerce a LongTable to a TreatmentResponseExperiment
as.RdCoerce a LongTable into a data.table.
Currently only supports coercing to data.table or data.frame
Coerce a data.table with the proper configuration attributes back to a LongTable
Value
The data in object, as the child-class
TreatmentResponseExperiment.
A data.table with the data from a LongTable.
data.table containing the data from the LongTable, with the
`longTableDataMapper' attribute containg the metadata needed to reverse
the coercing operation.
LongTable object configured with the longTableDataMapper
data.table with long format of data in from
data.frame with long format of data in from.
SummarizedExperiment with each assay as a BumpyMatrix
A TREDataMapper object.
Examples
data(clevelandSmall_cSet)
TRE <- as(treatmentResponse(clevelandSmall_cSet),
"TreatmentResponseExperiment")
TRE
#> <TreatmentResponseExperiment>
#> dim: 9 10
#> assays(2): sensitivity profiles
#> rownames(9): radiation:1:1 radiation:1:2 ... radiation:8:1 radiation:10:1
#> rowData(3): treatment1id treatment1dose replicate_id
#> colnames(10): CHP-212 IMR-32 KP-N-S19s ... SK-N-SH SNU-245 SNU-869
#> colData(2): sampleid rn
#> metadata(1): experiment_metadata
as(merckLongTable, 'data.table')
#> combination_name drug1id drug2id drug1dose drug2dose
#> <char> <char> <char> <num> <num>
#> 1: 5-FU & Bortezomib 5-FU Bortezomib 0.3500 0.00045
#> 2: 5-FU & Bortezomib 5-FU Bortezomib 0.3500 0.00045
#> 3: 5-FU & Bortezomib 5-FU Bortezomib 0.3500 0.00045
#> 4: 5-FU & Bortezomib 5-FU Bortezomib 0.3500 0.00045
#> 5: 5-FU & Bortezomib 5-FU Bortezomib 0.3500 0.00045
#> ---
#> 3796: geldanamycin & Topotecan geldanamycin Topotecan 0.0223 0.07750
#> 3797: geldanamycin & Topotecan geldanamycin Topotecan 0.0223 0.07750
#> 3798: geldanamycin & Topotecan geldanamycin Topotecan 0.0223 0.07750
#> 3799: geldanamycin & Topotecan geldanamycin Topotecan 0.0223 0.07750
#> 3800: geldanamycin & Topotecan geldanamycin Topotecan 0.0223 0.07750
#> sampleid batchid viability1 viability2 viability3 viability4
#> <char> <int> <num> <num> <num> <num>
#> 1: A2058 1 0.814 0.754 0.765 0.849
#> 2: A2780 1 0.214 0.195 0.186 0.223
#> 3: A375 1 1.064 1.080 1.082 1.009
#> 4: A427 1 0.675 0.582 0.482 0.516
#> 5: CAOV3 1 0.845 0.799 0.799 0.759
#> ---
#> 3796: A2058 1 0.090 0.043 0.112 0.103
#> 3797: A2780 1 0.025 0.022 0.029 0.023
#> 3798: A375 1 0.151 0.146 0.144 0.171
#> 3799: A427 1 0.142 0.166 0.124 0.175
#> 3800: CAOV3 1 0.091 0.084 0.134 0.119
#> mu/muMax_published X/X0_published
#> <num> <num>
#> 1: 0.880 0.847
#> 2: 0.384 0.426
#> 3: 1.033 1.047
#> 4: 0.676 0.638
#> 5: 0.708 0.667
#> ---
#> 3796: -0.187 0.193
#> 3797: -0.445 0.135
#> 3798: 0.090 0.283
#> 3799: -0.012 0.246
#> 3800: -1.935 0.017
dataTable <- as(merckLongTable, 'data.table')
print(attr(dataTable, 'longTableDataMapper')) # Method doesn't work without this
#> <LongTableDataMapper>
#> rawdata: NA
#> rowDataMap:
#> rowIDs: drug1id, drug2id, drug1dose, drug2dose
#> rowMeta: combination_name
#> colDataMap:
#> colIDs: sampleid, batchid
#> colMeta:
#> assayMap:
#> sensitivity:
#> keys: drug1id, drug2id, drug1dose, drug2dose, sampleid, batchid
#> values: viability1, viability2, viability3, viability4
#> profiles:
#> keys: drug1id, drug2id, drug1dose, drug2dose, sampleid, batchid
#> values: mu/muMax_published, X/X0_published
#> metadataMap: NA
as(dataTable, 'LongTable')
#> 2024-03-25 15:58:10 Building assay index...
#> 2024-03-25 15:58:10 Joining rowData to assayIndex...
#> 2024-03-25 15:58:11 Joining colData to assayIndex...
#> 2024-03-25 15:58:12 Joining assays to assayIndex...
#> 2024-03-25 15:58:13 Setting assayIndex key...
#> 2024-03-25 15:58:13 Building LongTable...
#>
#> <LongTable>
#> dim: 744 12
#> assays(2): sensitivity profiles
#> rownames(744): 5-FU:Bortezomib:0.35:0.00045 5-FU:Bortezomib:0.35:0.002 ... geldanamycin:Topotecan:0.0223:0.0223 geldanamycin:Topotecan:0.0223:0.0775
#> rowData(5): drug1id drug2id drug1dose drug2dose combination_name
#> colnames(12): A2058:1 A2058:3 A2780:1 ... CAOV3:1 CAOV3:2 CAOV3:3
#> colData(2): sampleid batchid
#> metadata(0): none
SE <- molecularProfilesSlot(clevelandSmall_cSet)[[1]]
as(SE, 'data.table')
#> Warning: Arguments in '...' ignored
#> Warning: Arguments in '...' ignored
#> Warning: Dropped S4 metadata during coercion to data.table!
#> Key: <.feature>
#> .feature .sample
#> <char> <char>
#> 1: ENSG00000000003 BUNDS_P_NCLE_RNA5_HG-U133_PLUS_2_B11_419860
#> 2: ENSG00000000003 BUNDS_P_NCLE_RNA5_HG-U133_PLUS_2_F07_419790
#> 3: ENSG00000000003 CASED_P_NCLE_RNA4_HG-U133_PLUS_2_G02_383638
#> 4: ENSG00000000003 CASED_P_NCLE_RNA4_HG-U133_PLUS_2_G03_383634
#> 5: ENSG00000000003 GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_C05_587588
#> ---
#> 8996: ENSG00000068394 GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_C05_587588
#> 8997: ENSG00000068394 GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_G02_587654
#> 8998: ENSG00000068394 NIECE_P_NCLE_RNA3_HG-U133_PLUS_2_G10_296152
#> 8999: ENSG00000068394 SILOS_P_NCLE_RNA9_HG-U133_PLUS_2_A04_523474
#> 9000: ENSG00000068394 WATCH_P_NCLE_RNA8_HG-U133_PLUS_2_B04_474582
#> exprs se.exprs samplename
#> <num> <lgcl> <char>
#> 1: 9.596987 NA BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_B11_419860
#> 2: 9.924551 NA BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_F07_419790
#> 3: 4.878338 NA CASED_p_NCLE_RNA4_HG-U133_Plus_2_G02_383638
#> 4: 4.865308 NA CASED_p_NCLE_RNA4_HG-U133_Plus_2_G03_383634
#> 5: 11.459240 NA GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588
#> ---
#> 8996: 8.119580 NA GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588
#> 8997: 8.683403 NA GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_G02_587654
#> 8998: 8.507980 NA NIECE_p_NCLE_RNA3_HG-U133_Plus_2_G10_296152
#> 8999: 8.810289 NA SILOS_p_NCLE_RNA9_HG-U133_Plus_2_A04_523474
#> 9000: 9.256034 NA WATCH_p_NCLE_RNA8_HG-U133_Plus_2_B04_474582
#> filename chiptype
#> <char> <char>
#> 1: BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_B11_419860.CEL.gz HG-U133_Plus_2
#> 2: BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_F07_419790.CEL.gz HG-U133_Plus_2
#> 3: CASED_p_NCLE_RNA4_HG-U133_Plus_2_G02_383638.CEL.gz HG-U133_Plus_2
#> 4: CASED_p_NCLE_RNA4_HG-U133_Plus_2_G03_383634.CEL.gz HG-U133_Plus_2
#> 5: GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588.CEL.gz HG-U133_Plus_2
#> ---
#> 8996: GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588.CEL.gz HG-U133_Plus_2
#> 8997: GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_G02_587654.CEL.gz HG-U133_Plus_2
#> 8998: NIECE_p_NCLE_RNA3_HG-U133_Plus_2_G10_296152.CEL.gz HG-U133_Plus_2
#> 8999: SILOS_p_NCLE_RNA9_HG-U133_Plus_2_A04_523474.CEL.gz HG-U133_Plus_2
#> 9000: WATCH_p_NCLE_RNA8_HG-U133_Plus_2_B04_474582.CEL.gz HG-U133_Plus_2
#> hybridization.date hybridization.hour file.day file.hour batch
#> <char> <char> <char> <char> <lgcl>
#> 1: 12/19/08 11:43:19 2009-01-07 13:06:03 NA
#> 2: 12/19/08 11:30:25 2009-01-07 13:05:45 NA
#> 3: 10/29/08 08:04:03 2008-11-04 14:19:49 NA
#> 4: 10/29/08 07:52:47 2008-11-04 14:19:49 NA
#> 5: 2010-05-21 17:07:46Z 2010-05-26 16:35:08 NA
#> ---
#> 8996: 2010-05-21 17:07:46Z 2010-05-26 16:35:08 NA
#> 8997: 2010-05-21 16:45:06Z 2010-05-26 16:35:21 NA
#> 8998: 07/15/08 12:54:10 2008-07-24 14:23:47 NA
#> 8999: 2009-12-08 20:44:59Z 2009-12-11 14:20:50 NA
#> 9000: 2009-08-14 17:15:45Z 2009-08-19 16:16:45 NA
#> sampleid CCLE.name Cell.line.primary.name
#> <char> <char> <char>
#> 1: KP-N-S19s KPNSI9S_AUTONOMIC_GANGLIA KP-N-SI9s
#> 2: SK-N-SH SKNSH_AUTONOMIC_GANGLIA SK-N-SH
#> 3: SK-N-FI SKNFI_AUTONOMIC_GANGLIA SK-N-FI
#> 4: SK-N-AS SKNAS_AUTONOMIC_GANGLIA SK-N-AS
#> 5: SNU-245 SNU245_BILIARY_TRACT SNU-245
#> ---
#> 8996: SNU-245 SNU245_BILIARY_TRACT SNU-245
#> 8997: IMR-32 IMR32_AUTONOMIC_GANGLIA IMR-32
#> 8998: CHP-212 CHP212_AUTONOMIC_GANGLIA CHP-212
#> 8999: MHH-NB-11 MHHNB11_AUTONOMIC_GANGLIA MHH-NB-11
#> 9000: NB1 NB1_AUTONOMIC_GANGLIA NB-1
#> Cell.line.aliases Gender Site.Primary Histology Hist.Subtype1
#> <char> <char> <char> <char> <char>
#> 1: KP-N-S19s M autonomic_ganglia neuroblastoma NS
#> 2: <NA> F autonomic_ganglia neuroblastoma NS
#> 3: SK-N-F1 M autonomic_ganglia neuroblastoma NS
#> 4: <NA> F autonomic_ganglia neuroblastoma NS
#> 5: NCI-SNU-245 <NA> biliary_tract carcinoma NS
#> ---
#> 8996: NCI-SNU-245 <NA> biliary_tract carcinoma NS
#> 8997: <NA> M autonomic_ganglia neuroblastoma NS
#> 8998: <NA> <NA> autonomic_ganglia neuroblastoma NS
#> 8999: <NA> M autonomic_ganglia neuroblastoma NS
#> 9000: <NA> M autonomic_ganglia neuroblastoma NS
#> Notes
#> <char>
#> 1: <NA>
#> 2: Identical lines: SH-SY5Y is a subclone derived from SK-N-SH and is identical to LAN-5
#> 3: <NA>
#> 4: <NA>
#> 5: <NA>
#> ---
#> 8996: <NA>
#> 8997: <NA>
#> 8998: <NA>
#> 8999: <NA>
#> 9000: <NA>
#> Source Expression.arrays
#> <char> <char>
#> 1: HSRRB BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_B11_419860
#> 2: ATCC BUNDS_p_NCLE_RNA5_HG-U133_Plus_2_F07_419790
#> 3: ATCC CASED_p_NCLE_RNA4_HG-U133_Plus_2_G02_383638
#> 4: ATCC CASED_p_NCLE_RNA4_HG-U133_Plus_2_G03_383634
#> 5: KCLB GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588
#> ---
#> 8996: KCLB GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_C05_587588
#> 8997: ATCC GILDS_p_NCLE_RNA11_Redo_HG-U133_Plus_2_G02_587654
#> 8998: ATCC NIECE_p_NCLE_RNA3_HG-U133_Plus_2_G10_296152
#> 8999: DSMZ SILOS_p_NCLE_RNA9_HG-U133_Plus_2_A04_523474
#> 9000: HSRRB WATCH_p_NCLE_RNA8_HG-U133_Plus_2_B04_474582
#> SNP.arrays Oncomap
#> <char> <char>
#> 1: FIEFS_p_NCLE_DNA_Affy5_GenomeWideSNP_6_H05_410924 yes
#> 2: BOWER_p_NCLE_DNAAffy8_GenomeWideSNP_6_B02_464602 yes
#> 3: FIEFS_p_NCLE_DNA_Affy5_GenomeWideSNP_6_F10_410970 yes
#> 4: FIEFS_p_NCLE_DNA_Affy5_GenomeWideSNP_6_C08_411042 yes
#> 5: QUAFF_p_NCLE_DNAAffy12_GenomeWideSNP_6_C12_592634 yes
#> ---
#> 8996: QUAFF_p_NCLE_DNAAffy12_GenomeWideSNP_6_C12_592634 yes
#> 8997: LOBBY_p_NCLE_DNAAffy6_GenomeWideSNP_6_C01_437320 yes
#> 8998: FASTS_p_NCLE_DNAAffy4_S_GenomeWideSNP_6_D02_335262 yes
#> 8999: AWASH_p_NCLE_DNAAffy10_GenomeWideSNP_6_H08_542886 yes
#> 9000: AWASH_p_NCLE_DNAAffy10_GenomeWideSNP_6_F10_542910 yes
#> Hybrid.Capture.Sequencing batchid
#> <char> <lgcl>
#> 1: yes NA
#> 2: yes NA
#> 3: yes NA
#> 4: yes NA
#> 5: yes NA
#> ---
#> 8996: yes NA
#> 8997: yes NA
#> 8998: yes NA
#> 8999: yes NA
#> 9000: yes NA
#> rownames.x Probe
#> <char> <char>
#> 1: BUNDS_P_NCLE_RNA5_HG-U133_PLUS_2_B11_419860 ENSG00000000003_at
#> 2: BUNDS_P_NCLE_RNA5_HG-U133_PLUS_2_F07_419790 ENSG00000000003_at
#> 3: CASED_P_NCLE_RNA4_HG-U133_PLUS_2_G02_383638 ENSG00000000003_at
#> 4: CASED_P_NCLE_RNA4_HG-U133_PLUS_2_G03_383634 ENSG00000000003_at
#> 5: GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_C05_587588 ENSG00000000003_at
#> ---
#> 8996: GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_C05_587588 ENSG00000068394_at
#> 8997: GILDS_P_NCLE_RNA11_REDO_HG-U133_PLUS_2_G02_587654 ENSG00000068394_at
#> 8998: NIECE_P_NCLE_RNA3_HG-U133_PLUS_2_G10_296152 ENSG00000068394_at
#> 8999: SILOS_P_NCLE_RNA9_HG-U133_PLUS_2_A04_523474 ENSG00000068394_at
#> 9000: WATCH_P_NCLE_RNA8_HG-U133_PLUS_2_B04_474582 ENSG00000068394_at
#> EnsemblGeneId EntrezGeneId Symbol GeneBioType BEST rownames.y
#> <char> <int> <char> <char> <lgcl> <char>
#> 1: ENSG00000000003 7105 TSPAN6 protein_coding TRUE ENSG00000000003
#> 2: ENSG00000000003 7105 TSPAN6 protein_coding TRUE ENSG00000000003
#> 3: ENSG00000000003 7105 TSPAN6 protein_coding TRUE ENSG00000000003
#> 4: ENSG00000000003 7105 TSPAN6 protein_coding TRUE ENSG00000000003
#> 5: ENSG00000000003 7105 TSPAN6 protein_coding TRUE ENSG00000000003
#> ---
#> 8996: ENSG00000068394 27238 GPKOW protein_coding TRUE ENSG00000068394
#> 8997: ENSG00000068394 27238 GPKOW protein_coding TRUE ENSG00000068394
#> 8998: ENSG00000068394 27238 GPKOW protein_coding TRUE ENSG00000068394
#> 8999: ENSG00000068394 27238 GPKOW protein_coding TRUE ENSG00000068394
#> 9000: ENSG00000068394 27238 GPKOW protein_coding TRUE ENSG00000068394
#> rownames.1
#> <char>
#> 1: ENSG00000000003
#> 2: ENSG00000000003
#> 3: ENSG00000000003
#> 4: ENSG00000000003
#> 5: ENSG00000000003
#> ---
#> 8996: ENSG00000068394
#> 8997: ENSG00000068394
#> 8998: ENSG00000068394
#> 8999: ENSG00000068394
#> 9000: ENSG00000068394
SE <- molecularProfilesSlot(clevelandSmall_cSet)[[1]]
as(SE, 'data.frame')
#> Warning: Arguments in '...' ignored
#> Warning: Arguments in '...' ignored
#> Warning: Dropped S4 metadata during coercion to data.table!