I have two matrices A and B, both have the same dimensions and are binary in nature. I want to overlap matrix A on matrix B.
Matrix A:
| Gene A | Gene B |
| -------- | ----------- |
| 0 | 1 |
| 0 | 1 |
Matrix B:
| Gene A | Gene B |
| -------- | ----------- |
| 1 | 0 |
| 0 | 0 |
Result:
Matrix C:
| Gene A | Gene B |
| -------- | ----------- |
| 1 | 1 |
| 0 | 1 |
The resultant matrix will also have the same dimension as the input.
How can this be done?
Please let me know.
Related
I am trying to make a simple clustering manually (without using any clustering algorithm) based on the distance between the points. I used the pearson correlation to calculate the distance:
c <- round(cor(t(df)), digits = 2)
d <- as.dist(1 - c)
I want to cluster all point that have a correlation greater than a certain threshold. For example 0,7. How could I cluster this data points in R?
The first rows and columns of my data frame look like this: (there are in total 188 entries and 31 columns
| | A1 | A2 | A3 | A4 | A5 |
| --- | --- | --- | --- | --- | --- |
| U00 | 0 | 0 | 0 | 0 | 0 |
| U01 | 0 | 0 | 84 | 0 | 0 |
| U02 | 0 | 1 | 0 | 0 | 0 |
| U03 | 0 | 0 | 0 | 0 | 0 |
| U04 | 0 | 0 | 0 | 0 | 0 |
| U05 | 0 | 0 | 0 | 0 | 0 |
| U06 | 0 | 0 | 0 | 0 | 0 |
and the dist:
| | U00 | U01 | U02 | U03 | U04 | U05 | U06 |
| | ------ | ------ | ------ | ------ | ------ | ------ | ------ |
| U01 | 0,05 | | | | | | |
| U02 | 1,04 | 1,05 | | | | | |
| U03 | 1,04 | 1,04 | 0,92 | | | | |
| U04 | 1,04 | 1,04 | 0,92 | 0,00 | | | |
| U05 | 1,04 | 1,04 | 0,92 | 0,00 | 0,00 | | |
| U06 | 1,04 | 1,04 | 0,92 | 0,00 | 0,00 | 0,00 | |
At the end I would like to habe an extra column in my data frame with the number of the cluster. Thank you in advance!
Things like this can be done using igraph package:
library(igraph)
threshold <- 0.7
graph_from_adjacency_matrix(abs(cor(df)) > threshold) %>%
components() %>%
membership() %>%
split(names(.), .)
note: I took absolute correlation, you can just remove abs.
I would like to assign groups to larger groups in order to assign them to cores for processing. I have 16 cores.This is what I have so far
test<-data_extract%>%group_by(group_id)%>%sample_n(16,replace = TRUE)
This takes staples OF 16 from each group.
This is an example of what I would like the final product to look like (with two clusters),all I really want is for the same group id to belong to the same cluster as a set number of clusters
________________________________
balance | group_id | cluster|
454452 | a | 1 |
5450441 | a | 1 |
5444531 | b | 1 |
5404051 | b | 1 |
5404501 | b | 1 |
5404041 | b | 1 |
544251 | b | 1 |
254252 | b | 1 |
541254 | c | 2 |
54123254 | d | 1 |
542541 | d | 1 |
5442341 | e | 2 |
541 | f | 1 |
________________________________
test<-data%>%group_by(group_id)%>% mutate(group = sample(1:16,1))
I have a table, that looks roughly like this:
| variable | observer1 | observer2 | observer3 | final |
| -------- | --------- | --------- | --------- | ----- |
| case1 | | | | |
| var1 | 1 | 1 | | |
| var2 | 3 | 3 | | |
| var3 | 4 | 5 | | 5 |
| case2 | | | | |
| var1 | 2 | | 2 | |
| var2 | 5 | | 5 | |
| var3 | 1 | | 1 | |
| case3 | | | | |
| var1 | | 2 | 3 | 2 |
| var2 | | 2 | 2 | |
| var3 | | 1 | 1 | |
| case4 | | | | |
| var1 | 1 | | 1 | |
| var2 | 5 | | 5 | |
| var3 | 3 | | 3 | |
Three colums for the observers, but only two are filled.
First I want to compute the IRR, so I need a table that has two columns without the empty cells like this:
| variable | observer1 | observer2 |
| -------- | --------- | --------- |
| case1 | | |
| var1 | 1 | 1 |
| var2 | 3 | 3 |
| var3 | 4 | 5 |
| case2 | | |
| var1 | 2 | 2 |
| var2 | 5 | 5 |
| var3 | 1 | 1 |
| case3 | | |
| var1 | 2 | 3 |
| var2 | 2 | 2 |
| var3 | 1 | 1 |
| case4 | | |
| var1 | 1 | 1 |
| var2 | 5 | 5 |
| var3 | 3 | 3 |
I try to use the tidyverse packages, but I'm not sure. Some 'ifelse()' magic may be easier.
Is there a clean and easy method to do something like this? Can anybody point me to the right function to use? Or just to a keyword to search for on stackoverflow? I found a lot of methods to remove whole empty columns or rows.
Edit: I removed the link to the original data. It was unnecessary. Thanks to Lamia for his working answer.
Out of your 3 columns observer1, observer2 and observer3, you sometimes have 2 non-NA values, 1 non-NA value, or 3 NA values.
If you want to merge your 3 columns, you could do:
res = data.frame(df$coding,t(apply(df[paste0("observer",1:3)],1,function(x) x[!is.na(x)][1:2])))
The apply function will return for each row the 2 non-NA values if there are 2, one non-NA value and one NA if there is only one value, and two NAs if there is no data in the row.
We then put this result in a dataframe with the first column (coding).
Programmers,
I have some difficulties in structuring my panel data set.
My panel data set, for the moment, has the following structure:
Exemplary here only with T = 2 and N = 3. (My real data set, however, is of size T = 6 and N = 20 000 000 )
Panel data structure 1:
Year | ID | Variable_1 | ... | Variable_k |
1 | 1 | A | ... | B |
1 | 2 | C | ... | D |
1 | 3 | E | ... | F |
2 | 1 | G | ... | H |
2 | 2 | I | ... | J |
2 | 3 | K | ... | L |
The desired structure is:
Panel data structure 2:
Year | ID | Variable_1 | ... | Variable_k |
1 | 1 | A | ... | B |
2 | 1 | G | ... | H |
1 | 2 | C | ... | D |
2 | 2 | I | ... | J |
1 | 3 | E | ... | F |
2 | 3 | K | ... | L |
This data structure represents the classic panel data structure, where the yearly observations over the whole period are structured for all individuals block by block.
My question: Is there any simple and efficient R-solution that changes the data structure from Table 1 to Table 2 for very large data sets (data.frame).
Thank you very much for all responses in advance!!
Enrico
You can reorder the rows of your dataframe using order():
df=df[order(df$ID,df$Year),]
I have 2 dataframes
Dataframe1:
| Cue | Ass_word | Condition | Freq | Cue_Ass_word |
1 | ACCENDERE | ACCENDINO | A | 1 | ACCENDERE_ACCENDINO
2 | ACCENDERE | ALLETTARE | A | 0 | ACCENDERE_ALLETTARE
3 | ACCENDERE | APRIRE | A | 1 | ACCENDERE_APRIRE
4 | ACCENDERE | ASCENDERE | A | 1 | ACCENDERE_ASCENDERE
5 | ACCENDERE | ATTIVARE | A | 0 | ACCENDERE_ATTIVARE
6 | ACCENDERE | AUTO | A | 0 | ACCENDERE_AUTO
7 | ACCENDERE | ACCENDINO | B | 2 | ACCENDERE_ACCENDINO
8 | ACCENDERE| ALLETTARE | B | 3 | ACCENDERE_ALLETTARE
9 | ACCENDERE| ACCENDINO | C | 2 | ACCENDERE_ACCENDINO
10 | ACCENDERE| ALLETTARE | C | 0 | ACCENDERE_ALLETTARE
Dataframe2:
| Group.1 | x
1 | ACCENDERE_ACCENDINO | 5
13 | ACCENDERE_FUOCO | 22
16 | ACCENDERE_LUCE | 10
24 | ACCENDERE_SIGARETTA | 6
....
I want to exclude from Dataframe1 all the rows that contain words (Cue_Ass_word) that are not reported in the column Group.1 in Dataframe2.
In other words, how can I subset Dataframe1 using the strings reported in Dataframe2$Group.1?
It's not quite clear what you mean, but is this what you need?
Dataframe1[!(Dataframe1$Cue_Ass_word %in% Dataframe2$Group1),]