使用 tapply 为数据子集生成方差

Question

我有一个基因列表，每个基因有 1-3 个探针，每个探针都有一个强度值。举例如下：

GENE_ID             Probes                  Intensity 
GENE:JGI_V11_100009 GENE:JGI_V11_1000090102 253.479375
GENE:JGI_V11_100009 GENE:JGI_V11_1000090202 712.235625
GENE:JGI_V11_100036 GENE:JGI_V11_1000360103 449.065625
GENE:JGI_V11_100036 GENE:JGI_V11_1000360203 641.341875
GENE:JGI_V11_100036 GENE:JGI_V11_1000360303 1237.07125
GENE:JGI_V11_100044 GENE:JGI_V11_1000440101 456.133125
GENE:JGI_V11_100045 GENE:JGI_V11_1000450101 369.790625
GENE:JGI_V11_100062 GENE:JGI_V11_1000620102 2839.97375
GENE:JGI_V11_100062 GENE:JGI_V11_1000620202 6384.55125

我想确定每个单独基因的探针之间的方差（因此对于每个基因我都有一个方差值）

我知道我应该使用 tapply() 函数，但不知道如何实现，除了：

tapply( , , var)

Answer 1

您可以使用 data.table 或 dplyr 来完成此操作。这是一个经典的group_by案例：

library(dplyr)
df %>% 
    group_by(GENE_ID) %>% 
    mutate(new_var = var(Intensity))


library(data.table)
setDT(df)
df[, new_var := var(Intensity), .(GENE_ID)]

两种情况下的输出都是：

               GENE_ID                  Probes Intensity   new_var
1: GENE:JGI_V11_100009 GENE:JGI_V11_1000090102  253.4794  105228.6
2: GENE:JGI_V11_100009 GENE:JGI_V11_1000090202  712.2356  105228.6
3: GENE:JGI_V11_100036 GENE:JGI_V11_1000360103  449.0656  168802.8
4: GENE:JGI_V11_100036 GENE:JGI_V11_1000360203  641.3419  168802.8
5: GENE:JGI_V11_100036 GENE:JGI_V11_1000360303 1237.0712  168802.8
6: GENE:JGI_V11_100044 GENE:JGI_V11_1000440101  456.1331        NA
7: GENE:JGI_V11_100045 GENE:JGI_V11_1000450101  369.7906        NA
8: GENE:JGI_V11_100062 GENE:JGI_V11_1000620102 2839.9738 6282014.8
9: GENE:JGI_V11_100062 GENE:JGI_V11_1000620202 6384.5513 6282014.8

Answer 2

这是基于 R 的经典 ave 案例。tapply returns 是一个与分组因子的唯一值长度相等的向量，ave returns 具有相同矢量长度 dataframe/matrix 列的分组平均值（或其他聚合）（按组重复值）：

gene_df$Probes_var <- ave(gene_df$Intensity, gene_df$GENE_ID, FUN=var)
gene_df

#               GENE_ID                  Probes Intensity Probes_var
# 1 GENE:JGI_V11_100009 GENE:JGI_V11_1000090102  253.4794   105228.6
# 2 GENE:JGI_V11_100009 GENE:JGI_V11_1000090202  712.2356   105228.6
# 3 GENE:JGI_V11_100036 GENE:JGI_V11_1000360103  449.0656   168802.8
# 4 GENE:JGI_V11_100036 GENE:JGI_V11_1000360203  641.3419   168802.8
# 5 GENE:JGI_V11_100036 GENE:JGI_V11_1000360303 1237.0712   168802.8
# 6 GENE:JGI_V11_100044 GENE:JGI_V11_1000440101  456.1331         NA
# 7 GENE:JGI_V11_100045 GENE:JGI_V11_1000450101  369.7906         NA
# 8 GENE:JGI_V11_100062 GENE:JGI_V11_1000620102 2839.9738  6282014.8
# 9 GENE:JGI_V11_100062 GENE:JGI_V11_1000620202 6384.5513  6282014.8

使用 tapply 为数据子集生成方差

Use tapply to generate variance for subsets of data

r

apply

tapply