Map.CN: Probe mapping of the copy number features of the training...

In iC10TrainingData: Training Datasets for iC10 Package

Description

Probe mapping of the copy number features of the training set.

Usage

data(Map.CN)

Format

A data frame with 38 observations on the following 8 variables.

Probe_ID

a character vector with the Illumina probe ids that flank the features

Gene_symbol

a factor with the hugo gene names

Ensembl_ID

a factor with the ensemble ids

Cytoband

a factor with the cytobands (on hg18)

Genomic_location_hg18

a factor with the genomic locations on hg18

chromosome_name_hg18

a numeric vector with the chromosome on hg18

start_position_hg18

a numeric vector with the start position on hg18

end_position_hg18

a numeric vector with the end position on hg18

Genomic_location_hg19

a factor with the genomic locations on hg19

chromosome_name_hg19

a numeric vector with the chromosome on hg19

start_position_hg19

a numeric vector with the start position on hg19

end_position_hg19

a numeric vector with the end position on hg19

Source

Curtis et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486:346-352.

Examples

data(Map.CN)
head(Map.CN)

Example output

                 Probe_ID Gene_symbol      Ensembl_ID Cytoband
ILMN_1699674 ILMN_1699674      ZNF703 ENSG00000183779    8p12a
ILMN_2378664 ILMN_2378664      ERLIN2 ENSG00000147475    8p12a
ILMN_1748908 ILMN_1748908       PROSC ENSG00000147471    8p12a
ILMN_1665554 ILMN_1665554        BRF2 ENSG00000104221    8p12a
ILMN_2409596 ILMN_2409596   RAB11FIP1 ENSG00000156675    8p12a
ILMN_1767324 ILMN_1767324    EIF4EBP1 ENSG00000187840    8p12a
                                         Genomic_location_hg18
ILMN_1699674                          chr8:37675195:37675244:+
ILMN_2378664 chr8:37714685:37714705:+,chr8:37717041:37717069:+
ILMN_1748908                          chr8:37756037:37756086:+
ILMN_1665554                          chr8:37820834:37820883:-
ILMN_2409596                          chr8:37837664:37837713:-
ILMN_1767324                          chr8:38036683:38036732:+
             chromosome_name_hg18 start_position_hg18 end_position_hg18
ILMN_1699674                    8            37675195          37675244
ILMN_2378664                    8            37714685          37714705
ILMN_1748908                    8            37756037          37756086
ILMN_1665554                    8            37820834          37820883
ILMN_2409596                    8            37837664          37837713
ILMN_1767324                    8            38036683          38036732
                Genomic_location_hg19 chromosome_name_hg19 start_position_hg19
ILMN_1699674 chr8:37556037:37556086:+                    8            37556037
ILMN_2378664 chr8:37595527:37595547:+                    8            37595527
ILMN_1748908 chr8:37636879:37636928:+                    8            37636879
ILMN_1665554 chr8:37701676:37701725:-                    8            37701676
ILMN_2409596 chr8:37718506:37718555:-                    8            37718506
ILMN_1767324 chr8:37917526:37917575:+                    8            37917526
             end_position_hg19
ILMN_1699674          37556086
ILMN_2378664          37595547
ILMN_1748908          37636928
ILMN_1665554          37701725
ILMN_2409596          37718555
ILMN_1767324          37917575

iC10TrainingData documentation built on May 2, 2019, 7:58 a.m.