- 一个基因表达矩阵，5个样本，每个样本5个重复，
每列分别为：geneid,S1_1,S1_2,S1_3,S1_4,S1_5,S2_1,S2_2,S2_3,S2_4,S2_5,……
$ cat a.tpm.tsvgene1 0.0 0.0 0.0 0.0 0.0 0.039595 0.0 0.000000 0.0 0.0 0.0 0.072418 0.136454 0.0 0.0 125.319084 206.183060 312.973907 1000.064026 535.770325 1111.690186 677.701477 747.069885 1043.504395 587.607422gene2 153.139114 80.315964 51.284149 81.167549 53.799297 19.027866 14.644533 24.061693 36.095894 15.593305 52.814518 47.106213 40.647087 40.411690 46.323067 64.985306 112.807793 64.820419 104.483238 87.293083 82.768089 91.885117 49.162933 58.043594 72.681511gene3 6.967771 11.112999 16.661377 12.513005 8.348808 3.606478 1.576240 3.155725 2.502464 2.007834 11.333991 8.626426 7.127884 3.307657 8.415873 3.260129 12.483765 11.294296 22.956882 13.596114 12.488963 9.070916 7.859025 11.917100 16.502171gene4 0.505876 0.386053 0.912009 1.151058 1.154426 0.850491 0.175352 0.269306 0.603023 0.486635 1.176807 0.524952 1.303849 0.030600 1.180763 0.071114 0.826968 0.919727 0.965852 0.624409 0.112988 0.484227 0.0 0.0 0.157508gene5 74.891602 106.629990 107.611679 184.312668 182.105698 54.929993 156.888580 95.991226 97.382843 57.194332 185.523758 85.128159 129.768570 87.086861 77.005058 87.280197 108.832001 142.719055 161.644943 158.324509 168.457855 196.658752 79.357765 77.824776 152.112717gene6 43.037334 25.253721 18.894386 26.046051 25.136530 10.951700 5.766452 9.901020 13.677269 9.700789 25.597813 18.042780 25.968611 23.025476 23.210535 35.266296 53.085224 33.859856 56.133625 38.710495 33.187077 27.609497 23.028906 26.431442 24.113132gene7 25.063200 56.035549 32.237309 72.436508 48.017216 26.486784 47.957367 44.359760 29.554129 25.999800 36.883751 17.445330 30.227165 15.413628 38.705254 30.413851 25.855337 19.630417 30.933867 35.670910 20.697100 30.442179 21.638878 36.755108 35.545338gene8 11.461951 13.055794 9.187213 14.815991 11.335137 4.229527 4.162697 4.990695 2.702080 3.662157 11.143311 7.460255 7.482308 11.640666 9.239034 15.579340 13.978998 11.687348 12.549714 8.261336 14.801984 15.432146 10.693584 8.335018 17.221148gene9 0.0 0.033566 0.329905 0.128400 0.042617 0.0 0.0 0.0 0.0 0.0 0.368945 0.033192 0.145969 0.000000 0.0 0.046507 0.149812 0.031563 2.481390 3.989131 0.000000 0.052335 0.093023 0.272024 0.965466
- 想求每个基因每个样本的平均值，用
awk实现的笨办法是将对应的列相加求平均值，($2+$3+$4+$5+$6)/5,($7+$8+$9+$10+$11)/5,......
$ awk '{print $1,($2+$3+$4+$5+$6)/5,($7+$8+$9+$10+$11)/5,($12+$13+$14+$15+$16)/5,($17+$18+$19+$20+$21)/5,($22+$23+$24+$25+$26)/5}' a.tpm.tsv | sort -k1 | column -tgene1 0 0.007919 0.0417744 436.062 833.515gene2 83.9412 21.8847 45.4605 86.878 70.9082gene3 11.1208 2.56975 7.76237 12.7182 11.5676gene4 0.821884 0.476961 0.843394 0.681614 0.150945gene5 131.11 92.4774 112.902 131.76 134.882gene6 27.6736 9.99945 23.169 43.4111 26.874gene7 46.758 34.8716 27.735 28.5009 29.0157gene8 11.9712 3.94943 9.39311 12.4113 13.2968gene9 0.106898 0 0.109621 1.33968 0.27657
- 下面这行代码，只需要改变参数
-v sample=5 -v repeat=5中的值，
如：6个样本，每个样本3个重复，改为-v sample=6 -v repeat=3即可。
这行代码，感觉上用处不大，但如果要封装
**Shell**脚本，还是挺方便的。
可以配合 脚本 | Shell | 任意n个样本表达量超过0.5视为表达 使用。
$ awk -v sample=5 -v repeat=5 '{for(i=1;i<=sample;i++){I=(i-1)*repeat;sum=0;for(j=1;j<=repeat;j++){sum+=$(I+j+1)};if(allsum[$1]=="")allsum[$1]=$1"\t"sum/repeat; else allsum[$1]=allsum[$1]"\t"sum/repeat}}END{for(k in allsum)print allsum[k]}' a.tpm.tsv | sort -k1 | column -tgene1 0 0.007919 0.0417744 436.062 833.515gene2 83.9412 21.8847 45.4605 86.878 70.9082gene3 11.1208 2.56975 7.76237 12.7182 11.5676gene4 0.821884 0.476961 0.843394 0.681614 0.150945gene5 131.11 92.4774 112.902 131.76 134.882gene6 27.6736 9.99945 23.169 43.4111 26.874gene7 46.758 34.8716 27.735 28.5009 29.0157gene8 11.9712 3.94943 9.39311 12.4113 13.2968gene9 0.106898 0 0.109621 1.33968 0.27657
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