Correlation Test loop in R
I am trying to create a data frame with p values and estimates that compares one gene to many different expression markers. My cor.test works when I use it on only one expression but when I try to loop it it breaks and gives me this error " 'x' and 'y' must have the same length".
I am wondering how to get this loop to work and build the data frame.
Below is what I am running through my loop and the code for the loop.
M3 <- ads$mean
Expression <- c("Exp1","Exp2","Exp3")
for (i in seq_along(Expression))
corr<-cor.test(M3, Expression[i], method = "pearson")
cor_df<-data.frame(Expression = Expression[i],pvalue = corr$p.value,
cor = corr$estimate)
r
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
add a comment |
I am trying to create a data frame with p values and estimates that compares one gene to many different expression markers. My cor.test works when I use it on only one expression but when I try to loop it it breaks and gives me this error " 'x' and 'y' must have the same length".
I am wondering how to get this loop to work and build the data frame.
Below is what I am running through my loop and the code for the loop.
M3 <- ads$mean
Expression <- c("Exp1","Exp2","Exp3")
for (i in seq_along(Expression))
corr<-cor.test(M3, Expression[i], method = "pearson")
cor_df<-data.frame(Expression = Expression[i],pvalue = corr$p.value,
cor = corr$estimate)
r
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
Expressionis a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation withExpression[i]doesn't make sense.
– PoGibas
Nov 12 '18 at 15:56
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57
add a comment |
I am trying to create a data frame with p values and estimates that compares one gene to many different expression markers. My cor.test works when I use it on only one expression but when I try to loop it it breaks and gives me this error " 'x' and 'y' must have the same length".
I am wondering how to get this loop to work and build the data frame.
Below is what I am running through my loop and the code for the loop.
M3 <- ads$mean
Expression <- c("Exp1","Exp2","Exp3")
for (i in seq_along(Expression))
corr<-cor.test(M3, Expression[i], method = "pearson")
cor_df<-data.frame(Expression = Expression[i],pvalue = corr$p.value,
cor = corr$estimate)
r
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
I am trying to create a data frame with p values and estimates that compares one gene to many different expression markers. My cor.test works when I use it on only one expression but when I try to loop it it breaks and gives me this error " 'x' and 'y' must have the same length".
I am wondering how to get this loop to work and build the data frame.
Below is what I am running through my loop and the code for the loop.
M3 <- ads$mean
Expression <- c("Exp1","Exp2","Exp3")
for (i in seq_along(Expression))
corr<-cor.test(M3, Expression[i], method = "pearson")
cor_df<-data.frame(Expression = Expression[i],pvalue = corr$p.value,
cor = corr$estimate)
r
r
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
asked Nov 12 '18 at 15:24
Dillon LloydDillon Lloyd
155
155
Expressionis a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation withExpression[i]doesn't make sense.
– PoGibas
Nov 12 '18 at 15:56
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57
add a comment |
Expressionis a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation withExpression[i]doesn't make sense.
– PoGibas
Nov 12 '18 at 15:56
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57
Expression is a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation with Expression[i] doesn't make sense.– PoGibas
Nov 12 '18 at 15:56
Expression is a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation with Expression[i] doesn't make sense.– PoGibas
Nov 12 '18 at 15:56
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57
add a comment |
1 Answer
1
active
oldest
votes
Based on your comment, if Exp1, Exp2, and Exp3 are columns in a data frame (df) then you can use something like this:
corr <- cor.test(M3, df[ ,Expression[i]], method = "pearson")
edited Nov 12 '18 at 16:47
989
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
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
Based on your comment, if Exp1, Exp2, and Exp3 are columns in a data frame (df) then you can use something like this:
corr <- cor.test(M3, df[ ,Expression[i]], method = "pearson")
edited Nov 12 '18 at 16:47
989
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
add a comment |
Based on your comment, if Exp1, Exp2, and Exp3 are columns in a data frame (df) then you can use something like this:
corr <- cor.test(M3, df[ ,Expression[i]], method = "pearson")
edited Nov 12 '18 at 16:47
989
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
add a comment |
Based on your comment, if Exp1, Exp2, and Exp3 are columns in a data frame (df) then you can use something like this:
corr <- cor.test(M3, df[ ,Expression[i]], method = "pearson")
edited Nov 12 '18 at 16:47
989
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
Based on your comment, if Exp1, Exp2, and Exp3 are columns in a data frame (df) then you can use something like this:
corr <- cor.test(M3, df[ ,Expression[i]], method = "pearson")
edited Nov 12 '18 at 16:47
989
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
edited Nov 12 '18 at 16:47
989
8,93251834
edited Nov 12 '18 at 16:47
989
8,93251834
edited Nov 12 '18 at 16:47
989
8,93251834
8,93251834
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
answered Nov 12 '18 at 16:11
pooja ppooja p
1197
1197
add a comment |
add a comment |
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Expressionis a character vector (Expression <- c("Exp1","Exp2","Exp3")) so to calculate correlation withExpression[i]doesn't make sense.– PoGibas
Nov 12 '18 at 15:56
Expression is calling names of numeric variables from my data frame. Does that not work properly when put into the cor test? It works when I do not put it into a loop.
– Dillon Lloyd
Nov 12 '18 at 15:57