Extract column name and match with another column Announcing the arrival of Valued Associate #679: Cesar Manara Planned maintenance scheduled April 17/18, 2019 at 00:00UTC (8:00pm US/Eastern) The Ask Question Wizard is Live! Data science time! April 2019 and salary with experienceHow to sort a dataframe by multiple column(s)Drop data frame columns by nameChanging column names of a data frameExtracting specific columns from a data frameCall apply-like function on each row of dataframe with multiple arguments from each rowFind highest threshold across 5 columns of dataframe to obtain n recordsCombine Dataframe Headers into Separate Dataframeobtaining max value in each column and printing associated column and row nameMake matrix from two columns of a dataframe and populate it by third without nested for loopExtract column positions that differ rows with duplicated pairs in a dataframe
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Extract column name and match with another column
Announcing the arrival of Valued Associate #679: Cesar Manara
Planned maintenance scheduled April 17/18, 2019 at 00:00UTC (8:00pm US/Eastern)
The Ask Question Wizard is Live!
Data science time! April 2019 and salary with experienceHow to sort a dataframe by multiple column(s)Drop data frame columns by nameChanging column names of a data frameExtracting specific columns from a data frameCall apply-like function on each row of dataframe with multiple arguments from each rowFind highest threshold across 5 columns of dataframe to obtain n recordsCombine Dataframe Headers into Separate Dataframeobtaining max value in each column and printing associated column and row nameMake matrix from two columns of a dataframe and populate it by third without nested for loopExtract column positions that differ rows with duplicated pairs in a dataframe
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I have a dataframe MutationsNumberTable like this
ACC BLCA BRCA CESC HGNC
1: 1 2 6 0 OPN4
2: 2 3 1 1 KLRB1
3: 2 23 4 5 SALL2
4: 1 8 5 7 PLCB2
The goal is to create a matrix where I have unique pairs "gene-cancer type" where a number in a table is greater than a threshold (let's say, 5):
Desired output:
HGNC Cancer
1: OPN4 CESC
2: SALL2 BRCA
3: SALL2 CESC
4: PLCB2 BLCA
5: PLCB2 BRCA
6: PLCB2 CESC
So far, I could come up with this:
n = ncol(MutationsNumberTable)
whereTrue = MutationsNumberTable[,1:(n-1)] >=threshold
but I have difficulties after to use these logical values to make a matrix I need. I tried
colnames(whereTrue)[whereTrue]
but it is not exactly what I need.
r filtering
asked Mar 8 at 15:04
lizavetalizaveta
657
add a comment |
I have a dataframe MutationsNumberTable like this
ACC BLCA BRCA CESC HGNC
1: 1 2 6 0 OPN4
2: 2 3 1 1 KLRB1
3: 2 23 4 5 SALL2
4: 1 8 5 7 PLCB2
The goal is to create a matrix where I have unique pairs "gene-cancer type" where a number in a table is greater than a threshold (let's say, 5):
Desired output:
HGNC Cancer
1: OPN4 CESC
2: SALL2 BRCA
3: SALL2 CESC
4: PLCB2 BLCA
5: PLCB2 BRCA
6: PLCB2 CESC
So far, I could come up with this:
n = ncol(MutationsNumberTable)
whereTrue = MutationsNumberTable[,1:(n-1)] >=threshold
but I have difficulties after to use these logical values to make a matrix I need. I tried
colnames(whereTrue)[whereTrue]
but it is not exactly what I need.
r filtering
asked Mar 8 at 15:04
lizavetalizaveta
657
add a comment |
I have a dataframe MutationsNumberTable like this
ACC BLCA BRCA CESC HGNC
1: 1 2 6 0 OPN4
2: 2 3 1 1 KLRB1
3: 2 23 4 5 SALL2
4: 1 8 5 7 PLCB2
The goal is to create a matrix where I have unique pairs "gene-cancer type" where a number in a table is greater than a threshold (let's say, 5):
Desired output:
HGNC Cancer
1: OPN4 CESC
2: SALL2 BRCA
3: SALL2 CESC
4: PLCB2 BLCA
5: PLCB2 BRCA
6: PLCB2 CESC
So far, I could come up with this:
n = ncol(MutationsNumberTable)
whereTrue = MutationsNumberTable[,1:(n-1)] >=threshold
but I have difficulties after to use these logical values to make a matrix I need. I tried
colnames(whereTrue)[whereTrue]
but it is not exactly what I need.
r filtering
asked Mar 8 at 15:04
lizavetalizaveta
657
I have a dataframe MutationsNumberTable like this
ACC BLCA BRCA CESC HGNC
1: 1 2 6 0 OPN4
2: 2 3 1 1 KLRB1
3: 2 23 4 5 SALL2
4: 1 8 5 7 PLCB2
The goal is to create a matrix where I have unique pairs "gene-cancer type" where a number in a table is greater than a threshold (let's say, 5):
Desired output:
HGNC Cancer
1: OPN4 CESC
2: SALL2 BRCA
3: SALL2 CESC
4: PLCB2 BLCA
5: PLCB2 BRCA
6: PLCB2 CESC
So far, I could come up with this:
n = ncol(MutationsNumberTable)
whereTrue = MutationsNumberTable[,1:(n-1)] >=threshold
but I have difficulties after to use these logical values to make a matrix I need. I tried
colnames(whereTrue)[whereTrue]
but it is not exactly what I need.
r filtering
r filtering
asked Mar 8 at 15:04
lizavetalizaveta
657
asked Mar 8 at 15:04
lizavetalizaveta
657
asked Mar 8 at 15:04
lizavetalizaveta
657
asked Mar 8 at 15:04
lizavetalizaveta
657
asked Mar 8 at 15:04
lizavetalizaveta
657
657
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
We can do a gather to 'long' format and then filter
library(dplyr)
library(tidyr)
gather(df1, Cancer, val, -HGNC) %>%
filter(val >= 5) %>%
select(-val)
Or using data.table
library(data.table)
setDT(df1)[, melt(.SD, id.var = 'HGNC')[value >= 5, .(HGNC, Cancer = variable)]]
answered Mar 8 at 15:06
akrunakrun
422k13209284
1
data.tableworked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).
– lizaveta
Mar 8 at 15:15
2
@lizaveta May beselectfrom another package is masking. Can you try%>% dplyr::select(-val)
– akrun
Mar 8 at 15:16
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
We can do a gather to 'long' format and then filter
library(dplyr)
library(tidyr)
gather(df1, Cancer, val, -HGNC) %>%
filter(val >= 5) %>%
select(-val)
Or using data.table
library(data.table)
setDT(df1)[, melt(.SD, id.var = 'HGNC')[value >= 5, .(HGNC, Cancer = variable)]]
answered Mar 8 at 15:06
akrunakrun
422k13209284
1
data.tableworked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).
– lizaveta
Mar 8 at 15:15
2
@lizaveta May beselectfrom another package is masking. Can you try%>% dplyr::select(-val)
– akrun
Mar 8 at 15:16
add a comment |
We can do a gather to 'long' format and then filter
library(dplyr)
library(tidyr)
gather(df1, Cancer, val, -HGNC) %>%
filter(val >= 5) %>%
select(-val)
Or using data.table
library(data.table)
setDT(df1)[, melt(.SD, id.var = 'HGNC')[value >= 5, .(HGNC, Cancer = variable)]]
answered Mar 8 at 15:06
akrunakrun
422k13209284
1
data.tableworked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).
– lizaveta
Mar 8 at 15:15
2
@lizaveta May beselectfrom another package is masking. Can you try%>% dplyr::select(-val)
– akrun
Mar 8 at 15:16
add a comment |
We can do a gather to 'long' format and then filter
library(dplyr)
library(tidyr)
gather(df1, Cancer, val, -HGNC) %>%
filter(val >= 5) %>%
select(-val)
Or using data.table
library(data.table)
setDT(df1)[, melt(.SD, id.var = 'HGNC')[value >= 5, .(HGNC, Cancer = variable)]]
answered Mar 8 at 15:06
akrunakrun
422k13209284
We can do a gather to 'long' format and then filter
library(dplyr)
library(tidyr)
gather(df1, Cancer, val, -HGNC) %>%
filter(val >= 5) %>%
select(-val)
Or using data.table
library(data.table)
setDT(df1)[, melt(.SD, id.var = 'HGNC')[value >= 5, .(HGNC, Cancer = variable)]]
answered Mar 8 at 15:06
akrunakrun
422k13209284
edited Mar 8 at 15:09
answered Mar 8 at 15:06
akrunakrun
422k13209284
answered Mar 8 at 15:06
akrunakrun
422k13209284
answered Mar 8 at 15:06
akrunakrun
422k13209284
422k13209284
1
data.tableworked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).
– lizaveta
Mar 8 at 15:15
2
@lizaveta May beselectfrom another package is masking. Can you try%>% dplyr::select(-val)
– akrun
Mar 8 at 15:16
add a comment |
1
data.tableworked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).
– lizaveta
Mar 8 at 15:15
2
@lizaveta May beselectfrom another package is masking. Can you try%>% dplyr::select(-val)
– akrun
Mar 8 at 15:16
1
1
data.table worked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).– lizaveta
Mar 8 at 15:15
data.table worked perfectly well, thanks a lot! But gather function gives an error: Error in select(., -val) : unused argument (-val).– lizaveta
Mar 8 at 15:15
2
2
@lizaveta May be
select from another package is masking. Can you try %>% dplyr::select(-val)– akrun
Mar 8 at 15:16
@lizaveta May be
select from another package is masking. Can you try %>% dplyr::select(-val)– akrun
Mar 8 at 15:16
add a comment |
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