我有一个包含很多行和至少13列的数据框。我需要将每一行与上一行进行比较,看看两列是否完全相同,其余各行是否不同。
如果两列中的两行相等,我想将这些行放在新的数据框中。
这是我的数据框。
前三行具有样本“ Sample”,但只有两行是相同的“ Gene”。第7行和第8行也具有相同的样本和基因。
我希望有一个新数据框,其中仅包含具有相同样本和相同基因的行。像这样:
我写了这段代码:
Vec_sample <- c()
Vec_genes <- c()
Vec_variants <- c()
Vec_chr <- c()
Vec_coordinate <- c()
Vec_aa <- c()
Vec_Rs <- c()
`%notin%` <- Negate(`%in%`)
for (row in 1:nrow(dataframe))
{
for (row_compare in 1:nrow(dataframe))
{
if ((dataframe$Gene[row] == dataframe$Gene[row_compare])
& (row != row_compare))
{
if ((dataframe$Sample[row] %notin% Vec_sample) &
(dataframe$Sample[row] == dataframe$Sample[row_compare]))
{
Vec_sample <- c(Vec_sample , dataframe$Sample[row])
Vec_sample <- c(Vec_sample , dataframe$Sample[row_compare])
Vec_genes <- c(Vec_genes, dataframe$Gene[row])
Vec_genes <- c(Vec_genes, dataframe$Gene[row_compare])
Vec_variants <- c(Vec_variants , dataframe$Variants[row])
Vec_variants <- c(Vec_variants , dataframe$Variants[row_compare])
Vec_chr <- c(Vec_chr , dataframe$Chr[row])
Vec_chr <- c(Vec_chr , dataframe$Chr[row_compare])
Vec_coordinate <- c(Vec_coordinate, dataframe$Coordinate[row])
Vec_coordinate <- c(Vec_coordinate, dataframe$Coordinate[row_compare])
Vec_aa <- c(Vec_aa , dataframe$aa[row])
Vec_aa <- c(Vec_aa , dataframe$aa[row_compare])
Vec_Rs <- c(Vec_Rs , dataframe$Rs[row])
Vec_Rs <- c(Vec_Rs , dataframe$Rs[row_compare])
}
}
}
}
最后,当循环结束时,我用结果创建一个数据框。
final_dataframe <- data.frame(Vec_sample, Vec_genes, Vec_variants, Vec_chr, Vec_coordinate, Vec_aa, Vec_Rs).
一切都是重复的,因为我需要一对相等的样本和基因(当然,其余信息也是如此)。 我写了两个for循环,因为我想将实际基因与另一个进行比较。
有问题吗?如果样本已经保存在向量“ Vec_sample”中,如果还有另一对样本相同,我的脚本将不会保存这对样本。 (例如,对于样本14-043,首先它将保存基因ALG9对,但是不会保存基因MNS1对。)
这是我的错误的新数据框。
我之所以说这样的例外,是因为当我运行两个循环时,该表将被检查一次以上,并且可以多次保存该基因并将其重复。
很抱歉,如果我的语法或编程方式效率低下,那我是从这个世界开始的,我并不是真正的专家。
我希望我对自己的解释很好。 预先非常感谢
我提供输入数据。
structure(list(Sample = c("14-043", "14-043", "14-043", "14-043",
"14-043", "14-043", "14-077", "14-077", "13-340", "15-642", "15-642",
"15-642", "12-975"), Gene = c("ALG9", "ALG10B", "ALG9", "SLC5A9",
"MNS1", "MNS1", "ALG9", "ALG9", "GPI", "MNS1", "HK3", "MNS1",
"HK3"), Variant = c("T>T/G", "C>A/G", "C>C/G", "A>A/T", "A>T/T",
"C>C/T", "T>T/G", "C>C/G", "C>G/G", "A>T/T", "T>T/A", "C>C/T",
"T>T/A"), Chr = c(4, 4, 4, 13, 2, 2, 4, 4, 20, 2, 8, 2, 8), Coordinate = c(23410158,
3422351, 23410451, 2341043423, 324652341, 3246520, 23410158,
23410451, 234541, 324652341, 23412341, 3246520, 23412341), aa = c("Gly44Thr",
"His8Pro", "Ser44Thr", "Thr4Pro", "Ala45Ala", "Ala45Leu", "Gly44Thr",
"Ser44Thr", "Phe3Ala", "Ala45Ala", "Val34His", "Ala45Leu", "Val34His"
), Rs = c("rs1715919", "rs1734532413", "rs1732413", "rs173240",
"rs12305", "rs10356", "rs1715919", "rs1732413", "rs12342", "rs12305",
"rs9997", "rs10356", "rs9997")), row.names = c(NA, -13L), class = "data.frame")
答案 0 :(得分:1)
如果我对您的理解正确,则可以使用dplyr:filter
和lead
使用lag
来检查上一行和下一行
df <- structure(list(Sample = c("14-043", "14-043", "14-043", "14-043",
"14-043", "14-077", "14-077", "13-340", "15-642", "15-642", "12-975"
), Gene = c("ALG9", "ALG9", "SLC5A9", "MNS1", "MNS1", "ALG9",
"ALG9", "GPI", "MNS1", "MNS1", "HK3"), Variant = c("T>T/G", "C>C/G",
"A>A/T", "A>T/T", "C>C/T", "T>T/G", "C>C/G", "C>G/G", "A>T/T",
"C>C/T", "T>T/A"), Chr = c(4, 4, 13, 2, 2, 4, 4, 20, 2, 2, 8),
Coordinate = c(23410158, 23410451, 2341043423, 324652341,
3246520, 23410158, 23410451, 234541, 324652341, 3246520,
23412341), aa = c("Gly44Thr", "Ser44Thr", "Thr4Pro", "Ala45Ala",
"Ala45Leu", "Gly44Thr", "Ser44Thr", "Phe3Ala", "Ala45Ala",
"Ala45Leu", "Val34His"), Rs = c("rs1715919", "rs1732413",
"rs173240", "rs12305", "rs10356", "rs1715919", "rs1732413",
"rs12342", "rs12305", "rs10356", "rs9997")), row.names = c(NA,
-11L), class = "data.frame")
library(tidyverse)
df %>% filter(Sample == lag(Sample) | Sample == lead(Sample),
Gene == lag(Gene) | Gene == lead(Gene))
#> Sample Gene Variant Chr Coordinate aa Rs
#> 1 14-043 ALG9 T>T/G 4 23410158 Gly44Thr rs1715919
#> 2 14-043 ALG9 C>C/G 4 23410451 Ser44Thr rs1732413
#> 3 14-043 MNS1 A>T/T 2 324652341 Ala45Ala rs12305
#> 4 14-043 MNS1 C>C/T 2 3246520 Ala45Leu rs10356
#> 5 14-077 ALG9 T>T/G 4 23410158 Gly44Thr rs1715919
#> 6 14-077 ALG9 C>C/G 4 23410451 Ser44Thr rs1732413
#> 7 15-642 MNS1 A>T/T 2 324652341 Ala45Ala rs12305
#> 8 15-642 MNS1 C>C/T 2 3246520 Ala45Leu rs10356
由reprex package(v0.3.0)于2020-08-11创建