Perl（或R或SQL）：計算字符串在列之間出現的頻率

Question

我有一個看起來像這樣的文本文件：

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

（每列都是一個人類基因，每個都包含可變數量的蛋白質（字符串，這里顯示為字母），可以與這些基因結合）。

我想要做的是計算每個字符串表示的列數，輸出該數字和所有列標題，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

我一直試圖弄清楚如何在Perl和R中做到這一點，但到目前為止還沒有成功。 謝謝你的幫助。

Answer 1

這個解決方案看起來有點像黑客，但它提供了所需的輸出。 它依賴於同時使用plyr和reshape包，但我確信你可以找到基本的R替代品。 訣竅在於，函數melt讓我們將數據展平為長格式，從而可以實現從那一點開始的簡單（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")

得到：

> 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，假設每列中的蛋白質不具有需要去除的重復。 （如果他們這樣做，則應該使用散列哈希值。）

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";
}

從stdin讀取，寫入stdout。

Answer 3

一個襯墊（或更確切地說是3個襯墊）

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

Answer 4

如果它不是很多列，你可以在sql中做這樣的事情。 您基本上將數據壓縮成2列衍生的蛋白質/基因表，然后根據需要進行總結。

;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，像這樣：

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

假設數據如下：

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');