Question

我在R中使用前列腺基因表达数据（http://icos.cs.nott.ac.uk/datasets/microarray.html）并尝试将所有条目转换为数字以编写相似性函数。如何使用表达式值将所有条目从因子转换为数值？如果我这样索引数据框，

> prostate[5,4]
[1] 3.17469778457247
2093 Levels: 0.133822364738809 ... normal

我只想要值3.17 ......

Answer 1

该文件在最后一行有字符数据。当R读取它时，所有因素都变成因素，因为它不是数字。在bash中你可以看到：

tail -2 prostate_preprocessed.txt
AFFX-YEL021w/URA3_at 3.31255956783592 4.05800228545385 4.26348960812486 4.2180869800299 4.90599509636775 4.33488048792038 4.96535865133757 4.35350385526143 4.18529970123263 3.85103067777549 4.03836053811841 3.70345720098741 4.11379278781317 4.01121240340167 4.68296544299334 4.33584797205546 4.16864882878781 4.32781853396998 3.85145280458377 3.76586006943253 4.67388887037993 3.87182653639402 3.74997314075837 3.94258426954186 ...
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但是你可以通过只读到倒数第二行（bash再次）来修复它：

wc -l prostate_preprocessed.txt
    2136 prostate_preprocessed.txt

现在在R中

：

> prostate=read.table("prostate_preprocessed.txt", nrows=2135)
> prostate[4,5]
[1] 6.379761

修改 ps它是一种奇怪的文件格式，因为您可能希望最后一行中的肿瘤值为列标题：

> cn=read.table("prostate_preprocessed.txt", skip=2135, colClasses="character") > colnames(prostate)<-cn[1,]

将基因表达数据转换为R中的数字

1 个答案: