RSAT - matrix-quality result

Analysis: matrix-quality result (21/03/2018 17:50)

matrix-quality result: LexA and CTCF matrices from RegulonDB 2015

Command: matrix-quality  -v 0 -html_title ' LexA and CTCF matrices from RegulonDB 2015 ' -ms $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/input_matrix -matrix_format transfac -pseudo 1 -seq LexA_peaks $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/sequence1.fasta -seq_format fasta -plot LexA_peaks nwd -seq CRP_binding_sites $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/sequence2.fasta -plot CRP_binding_sites nwd -perm LexA_peaks 1 -perm CRP_binding_sites 1 -bgfile $RSAT/public_html/data/genomes/Escherichia_coli_GCF_000005845.2_ASM584v2/oligo-frequencies/2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz -bg_format oligo-analysis -bg_pseudo 0.01 -archive -o $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002

Matrix name	Logo	HTML report
LexA.RegulonDB2012		report
CRP.RegulonDB2012		report

NWD curves

Plot	Table
	report
	report

NWD comparison heatmaps

Name	Image
Max NWD	PDF Table
Max NWD for Positve Scores	PDF Table
AUC on NWD	PDF Table
AUC on NWD for Positive Scores	PDF Table

nwd

Information: Merging NWD files with compare-scores perl-scripts/compare-scores -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_score_distrib_CRP_binding_sites_nwd.tab -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_score_distrib_LexA_peaks_nwd.tab -ic 1 -sc 4 -numeric -basename -o tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_nwd_LexA.RegulonDB2012_compare-scores.tab

Information: Merging NWD files with compare-scores perl-scripts/compare-scores -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/CRP.RegulonDB2012/matrix-quality_2018-03-21.175002_CRP.RegulonDB2012_score_distrib_CRP_binding_sites_nwd.tab -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/CRP.RegulonDB2012/matrix-quality_2018-03-21.175002_CRP.RegulonDB2012_score_distrib_LexA_peaks_nwd.tab -ic 1 -sc 4 -numeric -basename -o tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/CRP.RegulonDB2012/matrix-quality_2018-03-21.175002_CRP.RegulonDB2012_nwd_CRP.RegulonDB2012_compare-scores.tab

Information: Merging NWD files with compare-scores perl-scripts/compare-scores -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_score_distrib_CRP_binding_sites_nwd.tab -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/CRP.RegulonDB2012/matrix-quality_2018-03-21.175002_CRP.RegulonDB2012_score_distrib_CRP_binding_sites_nwd.tab -ic 1 -sc 4 -numeric -basename -o tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_nwd_CRP_binding_sites_compare-scores.tab

Information: R-command for generate NWD tables: cat R-scripts/matrix_quality_compare.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " mtx.quality.nwds.file = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_files.txt'; plot.folder = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_plot'; formats = 'pdf,png'; print.heatmap = '1' "

Full cmd: cat R-scripts/matrix_quality_compare.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " mtx.quality.nwds.file = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_files.txt'; plot.folder = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_plot'; formats = 'pdf,png'; print.heatmap = '1' " [1] "Boom1" [1] "Reading file for matrix and sequence LexA.RegulonDB2012 CRP_binding_sites" [1] "Reading file for matrix and sequence LexA.RegulonDB2012 LexA_peaks" [1] "Reading file for matrix and sequence CRP.RegulonDB2012 CRP_binding_sites" [1] "Reading file for matrix and sequence CRP.RegulonDB2012 LexA_peaks" [1] "Reading in files with nwd data" [1] "LexA.RegulonDB2012" [1] "CRP_binding_sites" "LexA_peaks" [1] "LexA.RegulonDB2012" [1] "CRP_binding_sites" [1] 0.13 [1] "LexA.RegulonDB2012" [1] "LexA_peaks" [1] 0.57 [1] "CRP.RegulonDB2012" [1] "CRP_binding_sites" "LexA_peaks" [1] "CRP.RegulonDB2012" [1] "CRP_binding_sites" [1] 0.3636364 [1] "CRP.RegulonDB2012" [1] "LexA_peaks" [1] 0.01363636 [[1]] [[1]][[1]] [1] 3.075e-05 [[1]][[2]] [1] 0.0008841 [[2]] [[2]][[1]] [1] 0.007450864 [[2]][[2]] [1] -0.0003688864

Information: Merging NWD files with compare-scores perl-scripts/compare-scores -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_score_distrib_LexA_peaks_nwd.tab -i tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/CRP.RegulonDB2012/matrix-quality_2018-03-21.175002_CRP.RegulonDB2012_score_distrib_LexA_peaks_nwd.tab -ic 1 -sc 4 -numeric -basename -o tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_nwd_LexA_peaks_compare-scores.tab

Information: R-command for generate NWD tables: cat R-scripts/matrix_quality_compare.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " mtx.quality.nwds.file = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_files.txt'; plot.folder = 'tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002_all_nwd_plot'; formats = 'pdf,png'; print.heatmap = '1' "