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In attempt to extract mismatches between the two data frames below I've already managed to create a new data frame in which mismatches are replaced.
What I need now is a list of mismatches:
dfA <- structure(list(animal1 = c("AA", "TT", "AG", "CA"), animal2 = c("AA", "TB", "AG", "CA"), animal3 = c("AA", "TT", "AG", "CA")), .Names = c("animal1", "animal2", "animal3"), row.names = c("snp1", "snp2", "snp3", "snp4"), class = "data.frame")
# > dfA
# animal1 animal2 animal3
# snp1 AA AA AA
# snp2 TT TB TT
# snp3 AG AG AG
# snp4 CA CA CA
dfB <- structure(list(animal1 = c("AA", "TT", "AG", "CA"), animal2 = c("AA", "TB", "AG", "DF"), animal3 = c("AA", "TB", "AG", "DF")), .Names = c("animal1", "animal2", "animal3"), row.names = c("snp1", "snp2", "snp3", "snp4"), class = "data.frame")
#> dfB
# animal1 animal2 animal3
#snp1 AA AA AA
#snp2 TT TB TB
#snp3 AG AG AG
#snp4 CA DF DF
To clarify the mismatches, here they are marked as 00's:
# animal1 animal2 animal3
# snp1 AA AA AA
# snp2 TT TB 00
# snp3 AG AG AG
# snp4 CA 00 00
I need the following output:
structure(list(snpname = structure(c(1L, 2L, 2L), .Label = c("snp2", "snp4"), class = "factor"), animalname = structure(c(2L, 1L, 2L), .Label = c("animal2", "animal3"), class = "factor"), alleledfA = structure(c(2L, 1L, 1L), .Label = c("CA", "TT"), class = "factor"), alleledfB = structure(c(2L, 1L, 1L), .Label = c("DF", "TB"), class = "factor")), .Names = c("snpname", "animalname", "alleledfA", "alleledfB"), class = "data.frame", row.names = c(NA, -3L))
# snpname animalname alleledfA alleledfB
#1 snp2 animal3 TT TB
#2 snp4 animal2 CA DF
#3 snp4 animal3 CA DF
So far I've been trying to extract additional data out of my lapply function which I use to replace the mismatches by zero, without success though. I also tried to write an ifelse function without success. Hope you guys can help me out here!
Eventually this will be run for data sets with a dimension of 100K by 1000, so efficiency is a pro
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Example 1: Check Whether Two Data Frames are Equal Using identical() Function. The RStudio console returns the logical value TRUE, i.e. our two data frames data1 and data2 are the same. This time, the RStudio console prints the logical value FALSE, i.e. data1 and data3 are not the same.
We can use the compare package in R. We can easily use this package to compare two data frames and check out the summary of what extent it is changed. The function comparedf() is used to compare two dataframes in R. The function takes two dataframes and then check them for comparison.
The compare method in pandas shows the differences between two DataFrames. It compares two data frames, row-wise and column-wise, and presents the differences side by side. The compare method can only compare DataFrames of the same shape, with exact dimensions and identical row and column labels.
This question has data.table tag, so here's my attempt using this package. First step is to convert row names to columns as data.table don't like those, then converting to long format after rbinding and setting an id per data set, finding where there are more than one unique value and converting back to a wide format
library(data.table)
setDT(dfA, keep.rownames = TRUE)
setDT(dfB, keep.rownames = TRUE)
dcast(melt(rbind(dfA,
dfB,
idcol = TRUE),
id = 1:2
)[,
if(uniqueN(value) > 1L) .SD,
by = .(rn, variable)],
rn + variable ~ .id)
# rn variable 1 2
# 1: snp2 animal3 TT TB
# 2: snp4 animal2 CA DF
# 3: snp4 animal3 CA DF
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