Commits

Giovanni Marco Dall'Olio committed bfca6e1

BEST: calculated a new property, largest component (n.vertices/n.components)

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logs/topscores/av_closeness

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-Excellent, Berwin!
-Specifically the part about why the bug never really triggers wrong behavior. Your mail should be saved in 'The Annals of R' ...
-   -- Martin Maechler (after Berwin A Turlach reported a buglet in 'spline_eval')
-      R-devel (July 2005)
-
-Loading required package: plyr
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-Attaching package: ‘reshape’
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-The following object(s) are masked from ‘package:plyr’:
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-    rename, round_any
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-Loading required package: foreach
-Loading required package: iterators
-Loading required package: parallel
-Loading required package: DBI
-Loading required package: methods
-Loading required package: gsubfn
-Loading required package: proto
-Loading required namespace: tcltk
-Loading Tcl/Tk interface ... done
-Loading required package: chron
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-Attaching package: ‘chron’
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-The following object(s) are masked from ‘package:foreach’:
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-    times
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-Loading required package: RSQLite
-Loading required package: RSQLite.extfuns
-<SQLiteConnection: DBI CON (11879, 0)> 
- [1] "chr10_w11.csv.gz" "chr11_w11.csv.gz" "chr12_w11.csv.gz" "chr13_w11.csv.gz" "chr14_w11.csv.gz" "chr15_w11.csv.gz" "chr16_w11.csv.gz" "chr17_w11.csv.gz" "chr18_w11.csv.gz" "chr19_w11.csv.gz"
-[11] "chr1_w11.csv.gz"  "chr20_w11.csv.gz" "chr21_w11.csv.gz" "chr22_w11.csv.gz" "chr2_w11.csv.gz"  "chr3_w11.csv.gz"  "chr4_w11.csv.gz"  "chr5_w11.csv.gz"  "chr6_w11.csv.gz"  "chr7_w11.csv.gz" 
-[21] "chr8_w11.csv.gz"  "chr9_w11.csv.gz" 
-[1] "parsing chromosome file results/tables/whole_chromosomes/w11/chr10_w11.csv.gz"
-   gene    continent distance_definition n_snps central_snp chromosome central_snp_position upstream_position downstream_position region_size distance_from_upstream_margin
-1 chr10         glob                   1     11 rs184176670         10                71086             77582               60523       17059                             0
-2 chr10 global_noAMR                   1     11 rs184176670         10                71086             77582               60523       17059                             0
-3 chr10          AFR                   1     11 rs184176670         10                71086             77582               60523       17059                             0
-4 chr10          ASN                   1     11 rs184176670         10                71086             77582               60523       17059                             0
-5 chr10          EUR                   1     11 rs184176670         10                71086             77582               60523       17059                             0
-6 chr10         glob                   1     11  rs61838968         10                71861             77585               60969       16616                           446
-  distance_from_downstream_margin n_datapoints av_datapoints_per_node n_vertices n_edges n_components av_path_length var_path_length diameter av_w_path_length av_w_path_length_inv av_degree
-1                       135446181         2184                26.3133         83     166            3         3.7648          2.0447        8           0.0508             179.3307    4.0000
-2                       135446181         1700                22.6667         75     141            3         3.7633          2.0886        8           0.0662             126.9671    3.7600
-3                       135446181          370                 7.7083         48      78            3         3.5217          2.1434        8           0.1282              62.8317    3.2500
-4                       135446181          572                15.8889         36      61            1         3.3222          1.9421        8           0.1638              95.3322    3.3889
-5                       135446181          758                18.0476         42      67            1         3.6945          2.3915        8           0.2176              51.7426    3.1905
-6                       135446178         2184                24.2667         90     177            1         4.0172          2.2757        8           0.0456             206.5524    3.9333
-  var_degree median_degree max_degree av_w_degree av_w_degree_inv av_closeness var_closeness median_closeness max_closeness density av_betweenness var_betweenness median_betweenness max_betweenness
-1     4.3373             3         10      0.0929       3079.9198       0.1728        0.0008           0.1756        0.2113  0.0488       107.9277       16284.090            56.2948        644.3637
-2     4.1824             3          9      0.0991       2194.7252       0.1727        0.0009           0.1766        0.2139  0.0508        96.8267       14757.870            41.1863        519.0389
-3     3.5625             3          9      0.1204        478.6339       0.1795        0.0014           0.1843        0.2315  0.0691        54.3750        4780.238            30.7798        342.9503
-4     2.2932             3          6      0.1503        750.9215       0.3077        0.0021           0.2966        0.4023  0.0968        40.6389        1561.870            24.7144        126.8731
-5     2.5351             3          7      0.1238        660.4461       0.2783        0.0022           0.2770        0.3981  0.0778        55.2381        5980.397            22.6081        300.9406
-6     4.0178             3         10      0.0854       2883.6916       0.2535        0.0012           0.2493        0.3490  0.0442       134.2667       27749.458            59.5551        817.1015
-    window whole_gene_nsnps
-1 window_0           585993
-2 window_0           585993
-3 window_0           585993
-4 window_0           585993
-5 window_0           585993
-6 window_1           585993
-[1] "filtering regions.."
-[1] "getting top scores"
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-[1] "wrote tops scores to results/tables/whole_chromosomes/topscores//av_closeness_topscores.csv , chromosome 10"
-[1] "getting quantiles"
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  |                                                                                                                                                                                                    
  |                                                                                                                                                                                              |   0%  chromosome central_snp_position central_snp upstream_position region_size continent current_property
-1         10                71086 rs184176670             77582       17059       AFR           0.1795
-2         10                71861  rs61838968             77585       16616       AFR           0.2619
-3         10                72922 rs184991562             78983       12657       AFR           0.2596
-4         10                74028 rs191858480             79160       11967       AFR           0.1985
-5         10                75794 rs140638708             90127       21594       AFR           0.1994
-6         10                77582  rs75914453             90164       19078       AFR           0.2140
-Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
-  index 585857 outside bounds
-Calls: ddply ... <Anonymous> -> .fun -> sort -> sort.default -> sort.int
-In addition: Warning messages:
-1: In scores$current_property > default_cutoffs[[network_property]] :
-  longer object length is not a multiple of shorter object length
-2: In scores$current_property > default_cutoffs[[network_property]] :
-  longer object length is not a multiple of shorter object length
-3: In scores$current_property > default_cutoffs[[network_property]] :
-  longer object length is not a multiple of shorter object length
-4: In scores$current_property > default_cutoffs[[network_property]] :
-  longer object length is not a multiple of shorter object length
-5: In scores$current_property > default_cutoffs[[network_property]] :
-  longer object length is not a multiple of shorter object length
-
-Execution halted