Question

我有一个看起来像这样的文本文件：

gene1   gene2   gene3
a       d       c
b       e       d
c       f       g
d       g       
        h
        i

（每列都是一个人类基因，每个都包含可变数量的蛋白质（字符串，在这里显示为字母），可以与这些基因结合）。

我想要做的是计算每个字符串表示的列数，输出该数字和所有列标题，如下所示：

a   1   gene1
b   1   gene1
c   2   gene1 gene3
d   3   gene1 gene2 gene3
e   1   gene2
f   1   gene2
g   2   gene2 gene3
h   1   gene2
i   1   gene2

我一直试图弄清楚如何在Perl和R中做到这一点，但到目前为止还没有成功。谢谢你的帮助。

Answer 1

这个解决方案似乎有点像黑客，但它提供了所需的输出。它依赖于同时使用plyr和reshape包，但我确信你可以找到基本的R替代品。诀窍在于函数melt允许我们将数据展平为长格式，从而允许从那一点开始轻松（ish）操作。

library(reshape)
library(plyr)

#Recreate your data
dat <- data.frame(gene1 = c(letters[1:4], NA, NA),
                  gene2 = letters[4:9],
                  gene3 = c("c", "d", "g", NA, NA, NA)
                  )

#Melt the data. You'll need to update this if you have more columns
dat.m <- melt(dat, measure.vars = 1:3)

#Tabulate counts
counts <- as.data.frame(table(dat.m$value))

#I'm not sure what to call this column since it's a smooshing of column names
otherColumn <- ddply(dat.m, "value", function(x) paste(x$variable, collapse = " "))

#Merge the two together. You could fix the column names above, or just deal with it here
merge(counts, otherColumn, by.x = "Var1", by.y = "value")

给出：

> merge(counts, otherColumn, by.x = "Var1", by.y = "value")
  Var1 Freq                V1
1    a    1             gene1
2    b    1             gene1
3    c    2       gene1 gene3
4    d    3 gene1 gene2 gene3
....

Answer 2

在perl中，假设每列中的蛋白质没有需要去除的重复。（如果他们这样做，则应该使用散列哈希值。）

use strict;
use warnings;

my $header = <>;
my %column_genes;
while ($header =~ /(\S+)/g) {
    $column_genes{$-[1]} = "$1";
}

my %proteins;
while (my $line = <>) {
    while ($line =~ /(\S+)/g) {
        if (exists $column_genes{$-[1]}) {
            push @{ $proteins{$1} }, $column_genes{$-[1]};
        }
        else {
            warn "line $. column $-[1] unexpected protein $1 ignored\n";
        }
    }
}

for my $protein (sort keys %proteins) {
    print join("\t",
        $protein,
        scalar @{ $proteins{$protein} },
        join(' ', sort @{ $proteins{$protein} } )
    ), "\n";
}

从stdin读取，写入stdout。

Answer 3

一个衬里（或更确切地说是3个衬里）

ddply(na.omit(melt(dat, m = 1:3)), .(value), summarize, 
     len = length(variable), 
     var = paste(variable, collapse = " "))

Answer 4

如果不是很多列，你可以在sql中做这样的事情。您基本上将数据压缩成2列衍生的蛋白质/基因表，然后根据需要进行总结。

;with cte as (
  select gene1 as protein, 'gene1' as gene
  union select gene2 as protein, 'gene2' as gene
  union select gene3 as protein, 'gene3' as gene
)

select protein, count(*) as cnt, group_concat(gene) as gene
from cte
group by protein

Answer 5

在mysql中，像这样：

select protein, count(*), group_concat(gene order by gene separator ' ') from gene_protein group by protein;

假设数据如下：

create table gene_protein (gene varchar(255) not null, protein varchar(255) not null);
insert into gene_protein values ('gene1','a'),('gene1','b'),('gene1','c'),('gene1','d');
insert into gene_protein values ('gene2','d'),('gene2','e'),('gene2','f'),('gene2','g'),('gene2','h'),('gene2','i');
insert into gene_protein values ('gene3','c'),('gene3','d'),('gene3','g');

Perl（或R或SQL）：计算字符串在列之间出现的频率

5 个答案: