lmObj: Example of a LowMACA object
In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Description
Usage
Format
Source
Examples
Description
An object of class LowMACA of the alignment and mapping of the homeobox domain.
It is the example used in the vignette.
Usage
1
data("lmObj")
Format
An object of class LowMACA
Source
Created by LowMACA package
Examples
1
2
3
Example output
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
sh: 1: /usr/bin/perl: Permission denied
sh: 1: /usr/bin/perl: Permission denied
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: In system(paste(perl, "-MXML::Simple -e 1"), intern = TRUE) :
running command '/usr/bin/perl -MXML::Simple -e 1' had status 126
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
XML::Simple module for perl is not installed.
If you don't want to install a local clustal omega and use the web service, XML::Simple is required
4: In system(paste(perl, "-MLWP -e 1"), intern = TRUE) :
running command '/usr/bin/perl -MLWP -e 1' had status 126
5: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
LWP module for perl is not installed.
If you don't want to install a local clustal omega and use the web service, LWP is required
Formal class 'LowMACA' [package "LowMACA"] with 4 slots
..@ arguments:List of 6
.. ..$ genes : NULL
.. ..$ pfam : chr "PF00046"
.. ..$ input :'data.frame': 28 obs. of 7 variables:
.. .. ..$ Gene_Symbol : Factor w/ 27 levels "ADNP","ALX1",..: 4 13 13 12 8 5 6 19 20 23 ...
.. .. ..$ Pfam_ID : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Entrez : Factor w/ 27 levels "1046","1406",..: 25 26 26 27 15 1 2 7 8 11 ...
.. .. ..$ Envelope_Start: chr [1:28] "79" "16" "102" "34" ...
.. .. ..$ Envelope_End : chr [1:28] "135" "70" "156" "90" ...
.. .. ..$ UNIPROT : Factor w/ 27 levels "ADNP_HUMAN","ALX1_HUMAN",..: 4 13 13 12 8 5 6 19 20 23 ...
.. .. ..$ AMINO_SEQ : chr [1:28] "HKERTSFTHQQYEELEALFSQTMFPDRNLQEKLALRLDLPESTVKVWFRNRRFKLKK" "RRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH" "RRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGVPESRVQIWFQNRRSRL" "RRNRTTFTLQQLEALEAVFAQTHYPDVFTREELAMKINLTEARVQVWFQNRRAKWRK" ...
.. ..$ mode : chr "pfam"
.. ..$ params :List of 7
.. .. ..$ mutation_type : chr "missense"
.. .. ..$ tumor_type : chr [1:7] "skcm" "stad" "ucec" "luad" ...
.. .. ..$ min_mutation_number: num 0
.. .. ..$ density_bw : num 0
.. .. ..$ clustal_cmd : chr "clustalo"
.. .. ..$ use_hmm : logi FALSE
.. .. ..$ datum : logi FALSE
.. ..$ parallelize:List of 2
.. .. ..$ getMutations : logi FALSE
.. .. ..$ makeAlignment: logi TRUE
..@ alignment:List of 4
.. ..$ ALIGNMENT:'data.frame': 1708 obs. of 8 variables:
.. .. ..$ domainID : Factor w/ 28 levels "ARGFX|PF00046|503582|79;135",..: 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Gene_Symbol : Factor w/ 27 levels "ADNP","ALX1",..: 4 4 4 4 4 4 4 4 4 4 ...
.. .. ..$ Pfam : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Entrez : Factor w/ 27 levels "1046","127343",..: 21 21 21 21 21 21 21 21 21 21 ...
.. .. ..$ Envelope_Start: num [1:1708] 79 79 79 79 79 79 79 79 79 79 ...
.. .. ..$ Envelope_End : num [1:1708] 135 135 135 135 135 135 135 135 135 135 ...
.. .. ..$ Align : int [1:1708] 1 2 3 4 5 6 7 8 9 10 ...
.. .. ..$ Ref : num [1:1708] 79 80 81 82 83 84 85 86 87 88 ...
.. ..$ SCORE :List of 2
.. .. ..$ DIST_MAT : num [1:28, 1:28] NA 36.4 34.5 50.9 26.3 ...
.. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. ..$ SUMMARY_SCORE:'data.frame': 28 obs. of 4 variables:
.. .. .. ..$ MEAN_SIMILARITY : num [1:28] 39.5 37.6 40.1 47.6 27.4 ...
.. .. .. ..$ MEDIAN_SIMILARITY: num [1:28] 38.6 36.4 40 43.9 26.3 ...
.. .. .. ..$ MAX_SIMILARITY : num [1:28] 54.4 54.5 54.5 78.9 80.7 ...
.. .. .. ..$ MIN_SIMILARITY : num [1:28] 21.1 18.2 23.6 21.1 17.5 ...
.. ..$ CLUSTAL :Formal class 'AAMultipleAlignment' [package "Biostrings"] with 3 slots
.. .. .. ..@ unmasked:Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
.. .. .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots
.. .. .. .. .. .. .. ..@ xp_list :List of 1
.. .. .. .. .. .. .. .. ..$ :<externalptr>
.. .. .. .. .. .. .. ..@ .link_to_cached_object_list:List of 1
.. .. .. .. .. .. .. .. ..$ :<environment: 0x559f23cfd7d8>
.. .. .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots
.. .. .. .. .. .. .. ..@ group : int [1:28] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. .. .. .. ..@ start : int [1:28] 1 62 123 184 245 306 367 428 489 550 ...
.. .. .. .. .. .. .. ..@ width : int [1:28] 61 61 61 61 61 61 61 61 61 61 ...
.. .. .. .. .. .. .. ..@ NAMES : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementType : chr "AAString"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ rowmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ colmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. ..$ df :'data.frame': 61 obs. of 2 variables:
.. .. ..$ consensus : Factor w/ 18 levels "A","D","E","F",..: 13 13 1 13 15 1 4 15 14 3 ...
.. .. ..$ conservation: num [1:61] 0.326 0.472 0.156 0.883 0.652 ...
..@ mutations:List of 3
.. ..$ data :'data.frame': 1389 obs. of 8 variables:
.. .. ..$ Entrez : int [1:1389] 3199 3213 91464 23316 127343 3232 23316 644168 139324 3199 ...
.. .. ..$ Gene_Symbol : chr [1:1389] "HOXA2" "HOXB3" "ISX" "CUX2" ...
.. .. ..$ Amino_Acid_Letter : chr [1:1389] "L" "S" "P" "R" ...
.. .. ..$ Amino_Acid_Position: num [1:1389] 298 123 186 874 165 ...
.. .. ..$ Amino_Acid_Change : chr [1:1389] "L298M" "S123F" "P186A" "R874C" ...
.. .. ..$ Mutation_Type : chr [1:1389] "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" ...
.. .. ..$ Sample : chr [1:1389] "SA236" "SA212" "SA229" "BR-M-166" ...
.. .. ..$ Tumor_Type : chr [1:1389] "brca" "brca" "brca" "brca" ...
.. ..$ freq :'data.frame': 7 obs. of 29 variables:
.. .. ..$ StudyID : Factor w/ 7 levels "brca","coadread",..: 1 2 3 4 5 6 7
.. .. ..$ Total_Sequenced_Samples: int [1:7] 1262 296 513 178 559 438 248
.. .. ..$ ADNP : int [1:7] 11 11 6 2 10 11 11
.. .. ..$ ALX1 : int [1:7] 2 4 10 6 3 7 8
.. .. ..$ ALX4 : int [1:7] 2 4 10 2 6 10 6
.. .. ..$ ARGFX : int [1:7] 3 5 9 0 19 2 2
.. .. ..$ CDX4 : int [1:7] 2 0 11 3 24 7 9
.. .. ..$ CRX : int [1:7] 3 4 9 3 13 9 4
.. .. ..$ CUX1 : int [1:7] 3 11 21 8 32 21 21
.. .. ..$ CUX2 : int [1:7] 7 9 19 3 59 21 7
.. .. ..$ DBX2 : int [1:7] 3 3 12 0 22 4 5
.. .. ..$ DLX5 : int [1:7] 3 3 12 4 8 7 1
.. .. ..$ DMBX1 : int [1:7] 2 3 5 2 23 3 7
.. .. ..$ DRGX : int [1:7] 5 5 4 2 16 2 3
.. .. ..$ DUXA : int [1:7] 2 2 8 6 12 3 5
.. .. ..$ ESX1 : int [1:7] 2 9 7 2 13 7 3
.. .. ..$ EVX2 : int [1:7] 0 2 6 2 14 12 7
.. .. ..$ HDX : int [1:7] 11 12 18 6 10 8 19
.. .. ..$ HLX : int [1:7] 3 10 7 4 7 6 8
.. .. ..$ HOXA1 : int [1:7] 3 4 11 3 14 7 9
.. .. ..$ HOXA2 : int [1:7] 5 2 14 1 7 2 5
.. .. ..$ HOXA3 : int [1:7] 1 5 11 4 18 8 3
.. .. ..$ HOXA5 : int [1:7] 3 4 19 0 9 3 1
.. .. ..$ HOXB1 : int [1:7] 0 0 14 4 14 6 2
.. .. ..$ HOXB3 : int [1:7] 4 2 14 3 10 4 2
.. .. ..$ HOXD3 : int [1:7] 2 3 8 3 9 7 6
.. .. ..$ ISL1 : int [1:7] 4 11 9 2 10 4 4
.. .. ..$ ISX : int [1:7] 3 2 5 5 27 2 5
.. .. ..$ LHX8 : int [1:7] 2 5 15 6 12 9 7
.. ..$ aligned: num [1:28, 1:61] 0 0 1 0 0 1 0 0 0 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. ..$ : NULL
..@ entropy : list()
LowMACA documentation built on Nov. 8, 2020, 8:14 p.m.
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Description Usage Format Source Examples
Description
An object of class LowMACA of the alignment and mapping of the homeobox domain. It is the example used in the vignette.
Usage
1 | data("lmObj")
|
Format
An object of class LowMACA
Source
Created by LowMACA package
Examples
1 2 3 |
Example output
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
sh: 1: /usr/bin/perl: Permission denied
sh: 1: /usr/bin/perl: Permission denied
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: In system(paste(perl, "-MXML::Simple -e 1"), intern = TRUE) :
running command '/usr/bin/perl -MXML::Simple -e 1' had status 126
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
XML::Simple module for perl is not installed.
If you don't want to install a local clustal omega and use the web service, XML::Simple is required
4: In system(paste(perl, "-MLWP -e 1"), intern = TRUE) :
running command '/usr/bin/perl -MLWP -e 1' had status 126
5: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
LWP module for perl is not installed.
If you don't want to install a local clustal omega and use the web service, LWP is required
Formal class 'LowMACA' [package "LowMACA"] with 4 slots
..@ arguments:List of 6
.. ..$ genes : NULL
.. ..$ pfam : chr "PF00046"
.. ..$ input :'data.frame': 28 obs. of 7 variables:
.. .. ..$ Gene_Symbol : Factor w/ 27 levels "ADNP","ALX1",..: 4 13 13 12 8 5 6 19 20 23 ...
.. .. ..$ Pfam_ID : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Entrez : Factor w/ 27 levels "1046","1406",..: 25 26 26 27 15 1 2 7 8 11 ...
.. .. ..$ Envelope_Start: chr [1:28] "79" "16" "102" "34" ...
.. .. ..$ Envelope_End : chr [1:28] "135" "70" "156" "90" ...
.. .. ..$ UNIPROT : Factor w/ 27 levels "ADNP_HUMAN","ALX1_HUMAN",..: 4 13 13 12 8 5 6 19 20 23 ...
.. .. ..$ AMINO_SEQ : chr [1:28] "HKERTSFTHQQYEELEALFSQTMFPDRNLQEKLALRLDLPESTVKVWFRNRRFKLKK" "RRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH" "RRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGVPESRVQIWFQNRRSRL" "RRNRTTFTLQQLEALEAVFAQTHYPDVFTREELAMKINLTEARVQVWFQNRRAKWRK" ...
.. ..$ mode : chr "pfam"
.. ..$ params :List of 7
.. .. ..$ mutation_type : chr "missense"
.. .. ..$ tumor_type : chr [1:7] "skcm" "stad" "ucec" "luad" ...
.. .. ..$ min_mutation_number: num 0
.. .. ..$ density_bw : num 0
.. .. ..$ clustal_cmd : chr "clustalo"
.. .. ..$ use_hmm : logi FALSE
.. .. ..$ datum : logi FALSE
.. ..$ parallelize:List of 2
.. .. ..$ getMutations : logi FALSE
.. .. ..$ makeAlignment: logi TRUE
..@ alignment:List of 4
.. ..$ ALIGNMENT:'data.frame': 1708 obs. of 8 variables:
.. .. ..$ domainID : Factor w/ 28 levels "ARGFX|PF00046|503582|79;135",..: 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Gene_Symbol : Factor w/ 27 levels "ADNP","ALX1",..: 4 4 4 4 4 4 4 4 4 4 ...
.. .. ..$ Pfam : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..$ Entrez : Factor w/ 27 levels "1046","127343",..: 21 21 21 21 21 21 21 21 21 21 ...
.. .. ..$ Envelope_Start: num [1:1708] 79 79 79 79 79 79 79 79 79 79 ...
.. .. ..$ Envelope_End : num [1:1708] 135 135 135 135 135 135 135 135 135 135 ...
.. .. ..$ Align : int [1:1708] 1 2 3 4 5 6 7 8 9 10 ...
.. .. ..$ Ref : num [1:1708] 79 80 81 82 83 84 85 86 87 88 ...
.. ..$ SCORE :List of 2
.. .. ..$ DIST_MAT : num [1:28, 1:28] NA 36.4 34.5 50.9 26.3 ...
.. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. ..$ SUMMARY_SCORE:'data.frame': 28 obs. of 4 variables:
.. .. .. ..$ MEAN_SIMILARITY : num [1:28] 39.5 37.6 40.1 47.6 27.4 ...
.. .. .. ..$ MEDIAN_SIMILARITY: num [1:28] 38.6 36.4 40 43.9 26.3 ...
.. .. .. ..$ MAX_SIMILARITY : num [1:28] 54.4 54.5 54.5 78.9 80.7 ...
.. .. .. ..$ MIN_SIMILARITY : num [1:28] 21.1 18.2 23.6 21.1 17.5 ...
.. ..$ CLUSTAL :Formal class 'AAMultipleAlignment' [package "Biostrings"] with 3 slots
.. .. .. ..@ unmasked:Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
.. .. .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots
.. .. .. .. .. .. .. ..@ xp_list :List of 1
.. .. .. .. .. .. .. .. ..$ :<externalptr>
.. .. .. .. .. .. .. ..@ .link_to_cached_object_list:List of 1
.. .. .. .. .. .. .. .. ..$ :<environment: 0x559f23cfd7d8>
.. .. .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots
.. .. .. .. .. .. .. ..@ group : int [1:28] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. .. .. .. ..@ start : int [1:28] 1 62 123 184 245 306 367 428 489 550 ...
.. .. .. .. .. .. .. ..@ width : int [1:28] 61 61 61 61 61 61 61 61 61 61 ...
.. .. .. .. .. .. .. ..@ NAMES : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementType : chr "AAString"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ rowmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ colmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. ..$ df :'data.frame': 61 obs. of 2 variables:
.. .. ..$ consensus : Factor w/ 18 levels "A","D","E","F",..: 13 13 1 13 15 1 4 15 14 3 ...
.. .. ..$ conservation: num [1:61] 0.326 0.472 0.156 0.883 0.652 ...
..@ mutations:List of 3
.. ..$ data :'data.frame': 1389 obs. of 8 variables:
.. .. ..$ Entrez : int [1:1389] 3199 3213 91464 23316 127343 3232 23316 644168 139324 3199 ...
.. .. ..$ Gene_Symbol : chr [1:1389] "HOXA2" "HOXB3" "ISX" "CUX2" ...
.. .. ..$ Amino_Acid_Letter : chr [1:1389] "L" "S" "P" "R" ...
.. .. ..$ Amino_Acid_Position: num [1:1389] 298 123 186 874 165 ...
.. .. ..$ Amino_Acid_Change : chr [1:1389] "L298M" "S123F" "P186A" "R874C" ...
.. .. ..$ Mutation_Type : chr [1:1389] "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" ...
.. .. ..$ Sample : chr [1:1389] "SA236" "SA212" "SA229" "BR-M-166" ...
.. .. ..$ Tumor_Type : chr [1:1389] "brca" "brca" "brca" "brca" ...
.. ..$ freq :'data.frame': 7 obs. of 29 variables:
.. .. ..$ StudyID : Factor w/ 7 levels "brca","coadread",..: 1 2 3 4 5 6 7
.. .. ..$ Total_Sequenced_Samples: int [1:7] 1262 296 513 178 559 438 248
.. .. ..$ ADNP : int [1:7] 11 11 6 2 10 11 11
.. .. ..$ ALX1 : int [1:7] 2 4 10 6 3 7 8
.. .. ..$ ALX4 : int [1:7] 2 4 10 2 6 10 6
.. .. ..$ ARGFX : int [1:7] 3 5 9 0 19 2 2
.. .. ..$ CDX4 : int [1:7] 2 0 11 3 24 7 9
.. .. ..$ CRX : int [1:7] 3 4 9 3 13 9 4
.. .. ..$ CUX1 : int [1:7] 3 11 21 8 32 21 21
.. .. ..$ CUX2 : int [1:7] 7 9 19 3 59 21 7
.. .. ..$ DBX2 : int [1:7] 3 3 12 0 22 4 5
.. .. ..$ DLX5 : int [1:7] 3 3 12 4 8 7 1
.. .. ..$ DMBX1 : int [1:7] 2 3 5 2 23 3 7
.. .. ..$ DRGX : int [1:7] 5 5 4 2 16 2 3
.. .. ..$ DUXA : int [1:7] 2 2 8 6 12 3 5
.. .. ..$ ESX1 : int [1:7] 2 9 7 2 13 7 3
.. .. ..$ EVX2 : int [1:7] 0 2 6 2 14 12 7
.. .. ..$ HDX : int [1:7] 11 12 18 6 10 8 19
.. .. ..$ HLX : int [1:7] 3 10 7 4 7 6 8
.. .. ..$ HOXA1 : int [1:7] 3 4 11 3 14 7 9
.. .. ..$ HOXA2 : int [1:7] 5 2 14 1 7 2 5
.. .. ..$ HOXA3 : int [1:7] 1 5 11 4 18 8 3
.. .. ..$ HOXA5 : int [1:7] 3 4 19 0 9 3 1
.. .. ..$ HOXB1 : int [1:7] 0 0 14 4 14 6 2
.. .. ..$ HOXB3 : int [1:7] 4 2 14 3 10 4 2
.. .. ..$ HOXD3 : int [1:7] 2 3 8 3 9 7 6
.. .. ..$ ISL1 : int [1:7] 4 11 9 2 10 4 4
.. .. ..$ ISX : int [1:7] 3 2 5 5 27 2 5
.. .. ..$ LHX8 : int [1:7] 2 5 15 6 12 9 7
.. ..$ aligned: num [1:28, 1:61] 0 0 1 0 0 1 0 0 0 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
.. .. .. ..$ : NULL
..@ entropy : list()
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