从多个独立变量创建一个合并变量

Question

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我有一个从PCR模板软件导出的文件。我已经对所有等位基因的调用进行了编码，现在已经将它们合并到一个数据帧中。

我需要创建一个新的变量来合并3个等位基因(G1-1、G1-2和G2)，以获得最终的基因型。

然后，我需要计算等位基因的出现次数，以生成我需要生成的其他3个APOL1风险变量。

Allele logic for final genotype:

+/G2 = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) & (occurence of (G2) at either G2-1 or G2-2)

+/+ = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) & (G2-1(+) & G2-2(+))

G2/G2 = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) & (G2-1(G2) & G2-2(G2))

G1^GM/+ = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & (occurence of (G1^I384M) at either G1-2-1 or G1-2-2) & (G2-1(+) & G2-2(+))

G1^G+/+ = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & (G1-2-1(+) & G1-2-2(+)) & (G2-1(+) & G2-2(+))

G1^GM/G1^GM = (occurence of (G1^S342G) at both G1-1-1 or G1-1-2) & (occurence of (G1^I384M) at both G1-2-1 or G1-2-2) & (G2-1(+) & G2-2(+))

G1^GM/G2 = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & (occurence of (G1^I384M) at either G1-2-1 or G1-2-2) & (occurence of (G2) at either G2-1 or G2-2)

G1^G+/G2 = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & (G1-2-1(+) & G1-2-2(+) & (occurence of (G2) at either G2-1 or G2-2)

Original dataframe

Final dataframe needed

原始数据帧结构

Classes ‘tbl_df’, ‘tbl’ and 'data.frame':   28 obs. of  6 variables:
 $ G1-1-1   : chr  "+" "+" "+" "+" ...
 $ G1-1-2   : chr  "+" "+" "+" "+" ...
 $ G1-2-1   : chr  "+" "+" "+" "+" ...
 $ G1-2-2   : chr  "+" "+" "+" "+" ...
 $ G2-1     : chr  "+" "+" "+" "+" ...
 $ G2-2     : chr  "G2" "+" "G2" "G2" ...

The APOL1 Risk variables logic is below:

If (+/+) categorize as 1 in "no APOL1 Risk Alleles"

If (+/G2) or (G1^GM/+) or (G1^G+/+) categorize as 1 in "1 APOL1 Risk Alleles"

If (G1^GM/G1^GM) or (G1^GM/G2) or (G2/G2) categorize as 1 in "2 APOL1 Risk Alleles" 

Answer 1

您可以使用dplyr函数轻松地实现逻辑。

在给定的情况下实现逻辑应该是执行该逻辑所需的代码；

library(dplyr)

data <-
  data.frame(
    G1_1_1 = c("+", "+", "+", "+", "+", "+", "+", "G1S342G", "+", "G1S342G", "+", "+", "+", "+",
               "G1S342G", "G1S342G", "+", "G1S342G", "+", "+", "+", "G1S342G", "+", "+",
               "G1S342G", "+", "G1S342G", "G1S342G"),
    G1_1_2 = c("+", "+", "+", "+", "+", "+", "+", "G1S342G", "+", "+", "+", "+", "+", "+", "+",
               "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+"),
    G1_2_1 = c("+", "+", "+", "+", "+", "+", "+", "G1I384M", "+", "G1I384M", "+", "+", "+", "+",
               "G1I384M", "G1I384M", "+", "G1I384M", "+", "+", "+", "+", "+", "+", "G1I384M",
               "+", "G1I384M", "G1I384M"),
    G1_2_2 = c("+", "+", "+", "+", "+", "+", "+", "G1I384M", "+", "+", "+", "+", "+", "+", "+",
               "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+"),
    G2_1 = c("+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+",
             "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+"),
    G2_2 = c("G2", "+", "G2", "G2", "G2", "+", "+", "+", "G2", "G2", "+", "G2", "+", "G2", "G2",
             "+", "+", "+", "G2", "+", "G2", "+", "+", "+", "+", "+", "+", "+"),
    stringsAsFactors = FALSE
  )

result <-
  data %>% mutate(
    "Final genotype of APOL1" = 
      case_when(
        # +/+ = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) & (G2-1(+) & G2-2(+))
        G1_1_1 == "+" & G1_1_2 == "+" & G1_2_1 == "+" & 
          G1_2_2 == "+" & G2_1 == "+" & G2_2 == "+" ~ "+/+",

        # G2/G2 = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) & (G2-1(G2) & G2-2(G2))
        G1_1_1 == "+" & G1_1_2 == "+" & G1_2_1 == "+" & 
          G1_2_2 == "+" & G2_1 == "G2" & G2_2 == "G2" ~ "G2/G2",

        # G1^GM/G1^GM = (occurence of (G1^S342G) at both G1-1-1 or G1-1-2) 
        # & (occurence of (G1^I384M) at both G1-2-1 or G1-2-2) & (G2-1(+) & G2-2(+))
        G1_1_1 == "G1S342G" & G1_1_2 == "G1S342G" & G1_2_1 == "G1I384M" & 
          G1_2_2 == "G1I384M" & G2_1 == "+" & G2_2 == "+" ~ "G1GM/G1GM",

        #+/G2 = (G1-1-1(+) & G1-1-2(+)) & (G1-2-1(+) & G1-2-2(+)) 
        #& (occurence of (G2) at either G2-1 or G2-2)
        G1_1_1 == "+" & G1_1_2 == "+" & G1_2_1 == "+" & 
          G1_2_2 == "+" & (G2_1 == "G2" | G2_2 == "G2") ~ "+/G2",

        # G1^G+/+ = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) 
        # & (G1-2-1(+) & G1-2-2(+)) & (G2-1(+) & G2-2(+))
        (G1_1_1 == "G1S342G" | G1_1_2 == "G1S342G") & G1_2_1 == "+" & 
          G1_2_2 == "+" & G2_1 == "+" & G2_2 == "+" ~ "G1G+/+",

        # G1^G+/G2 = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) 
        # & (G1-2-1(+) & G1-2-2(+) & (occurence of (G2) at either G2-1 or G2-2)
        (G1_1_1 == "G1S342G" | G1_1_2 == "G1S342G") & G1_2_1 == "+" & 
          G1_2_2 == "+" & (G2_1 == "G2" | G2_2 == "G2") ~ "G1G+/G2",

        # G1^GM/+ = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & 
        # (occurence of (G1^I384M) at either G1-2-1 or G1-2-2) & (G2-1(+) & G2-2(+))
        (G1_1_1 == "G1S342G" | G1_1_2 == "G1S342G") & 
          (G1_2_1 == "G1I384M" | G1_2_2 == "G1I384M") & 
          G2_1 == "+" & G2_2 == "+" ~ "G1GM/+",

        # G1^GM/G2 = (occurence of (G1^S342G) at either G1-1-1 or G1-1-2) & 
        # (occurence of (G1^I384M) at either G1-2-1 or G1-2-2) & 
        # (occurence of (G2) at either G2-1 or G2-2)
        (G1_1_1 == "G1S342G" | G1_1_2 == "G1S342G") & 
          (G1_2_1 == "G1I384M" | G1_2_2 == "G1I384M") & 
          (G2_1 == "G2" | G2_2 == "G2") ~ "G1GM/G2",

        TRUE ~ NA_character_),

    "no APOL1 Risk Alleles" = ifelse(`Final genotype of APOL1` == "+/+", 1, NA),

    "1 APOL1 Risk Alleles" = 
      ifelse(`Final genotype of APOL1` %in% c("+/G2", "G1GM/+", "G1G+/+"), 1, NA),

    "2 APOL1 Risk Alleles" =
      ifelse(`Final genotype of APOL1` %in% c("G1GM/G1GM", "G1GM/G2", "G2/G2"), 1, NA),
  )

glimpse(result)

# Observations: 28
# Variables: 10
# $ G1_1_1                    <chr> "+", "+", "+", "+", "+", "+", "+", "G1S342G", "+", "G1S342G", ...
# $ G1_1_2                    <chr> "+", "+", "+", "+", "+", "+", "+", "G1S342G", "+", "+", "+", "...
# $ G1_2_1                    <chr> "+", "+", "+", "+", "+", "+", "+", "G1I384M", "+", "G1I384M", ...
# $ G1_2_2                    <chr> "+", "+", "+", "+", "+", "+", "+", "G1I384M", "+", "+", "+", "...
# $ G2_1                      <chr> "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+...
# $ G2_2                      <chr> "G2", "+", "G2", "G2", "G2", "+", "+", "+", "G2", "G2", "+", "...
# $ `Final genotype of APOL1` <chr> "+/G2", "+/+", "+/G2", "+/G2", "+/G2", "+/+", "+/+", "G1GM/G1G...
# $ `no APOL1 Risk Alleles`   <dbl> NA, 1, NA, NA, NA, 1, 1, NA, NA, NA, 1, NA, 1, NA, NA, NA, 1, ...
# $ `1 APOL1 Risk Alleles`    <dbl> 1, NA, 1, 1, 1, NA, NA, NA, 1, NA, NA, 1, NA, 1, NA, 1, NA, 1,...
# $ `2 APOL1 Risk Alleles`    <dbl> NA, NA, NA, NA, NA, NA, NA, 1, NA, 1, NA, NA, NA, NA, 1, NA, N...