tab format
[tab]sample1[tab]sample2[tab]sample3
gene1[tab]1.0[tab]2.0[tab]3.0
gene2[tab]4.0[tab]5.0[tab]6.0
gene3[tab]7.0[tab]8.0[tab]9.0
1以下を1にする
perl ExpCnUtility/perl/expression.pl -f 1 exp.tab > exp2.tab
log10にスケールを変換
perl ExpCnUtility/perl/expression.pl -l 10 exp.tab > exp2.tab
rowごとに（つまり各遺伝子ごとに）分散１平均0に標準化
perl ExpCnUtility/perl/expression.pl -r exp.tab > exp2.tab
columごと（つまり各サンプルごとに）平均100にそろえる
perl ExpCnUtility/perl/expression.pl -m 100 exp.tab > exp2.tab
varianceの高い5000遺伝子にしぼる
perl ExpCnUtility/perl/expression.pl -v 5000 exp.tab > exp2.tab
annotation.chipを使ってprobe IDからgene symbolに変換する
perl perl/expression.pl -a annotation.chip -R exp.tab > exp2.tab
seg format https://software.broadinstitute.org/software/igv/SEG
長さ100000未満のsegmentを除く
perl ExpCnUtility/perl/segment.pl -S 100000 cn.seg > cn2.seg
>0.1を1 ≦0.1 を0
perl ExpCnUtility/perl/segment.pl -B 0.1 cn.seg > cn2.seg
<-0.1を1 ≧-0.1 を0
perl ExpCnUtility/perl/segment.pl -L -0.1 cn.seg > cn2.seg
>0.1を1 <-0.1を-1 それ以外を0
perl ExpCnUtility/perl/segment.pl -B 0.1 -L -0.1 cn.seg > cn2.seg
> 90 percentile を1 ≦ 90 percentile を0
perl ExpCnUtility/perl/segment.pl -G 0.9 cn.seg > cn2.seg
< 10 percentile を1 ≧ 10 percentile を0
perl ExpCnUtility/perl/segment.pl -K 0.1 cn.seg > cn2.seg
> 90 percentile を1 < 10 percentile を-1 それ以外を0
perl ExpCnUtility/perl/segment.pl -G 0.9 -K 0.1 cn.seg > cn2.seg
XY染色体を除く
perl ExpCnUtility/perl/segment.pl -r cn.seg > cn2.seg
segmentのギャップを埋める
perl ExpCnUtility/ExpCnUtility/perl/segment.pl -f cn.seg > cn.fld.seg
遺伝子ごとのコピー数をもとめる
perl ExpCnUtility/perl/segment.pl -M -b ExpCnUtility/data/symbol.hg19.bed cn.fld.seg > cn.gene.tab
armごとのコピー数をもとめる
perl ExpCnUtility/perl/segment.pl -M -b ExpCnUtility/data/arm.hg19.bed cn.fld.seg > cn.arm.tab
約10000個のprobe数のmatrixを作る
perl ExpCnUtility/perl/segment.pl -M -n 10000 cn.fld.seg > cn.10000.tab