Hi R users,
I generated a square correlation matrix for the dat dataframe below;
dat<-data.frame(g1=c(1,0,0,1,1,1,0,0,0),
g2=c(0,1,0,1,0,1,1,0,0),
g3=c(1,1,0,0,0,1,0,0,0),
g4=c(0,1,0,1,1,1,1,1,0))
library("Hmisc")
dat.rcorr = rcorr(as.matrix(dat))
dat.r <-round(dat.rcorr$r,2)
however, I want to modify this correlation calculation;
my dat has more than 1000 rows and 22 columns;
in each column, less than 10% values are 1, most of them are 0;
so I want to remove a row with value of zero in both columns when calculate
correlation between two columns.
I just want to check whether those values of 1 are correlated between two
columns.
Please look at my code in the following;
cor.4gene <-matrix(0,nrow=4*4, ncol=4)
for (i in 1:4){
#i=1
for (j in 1:4) {
#j=1
d <-dat[,c(i,j)]%>%
filter(eval(as.symbol(colnames(dat)[i]))!=0 |
eval(as.symbol(colnames(dat)[j]))!=0)
c <-cor.test(d[,1],d[,2])
cor.4gene[i*j,]<-c(colnames(dat)[i],colnames(dat)[j],
c$estimate,c$p.value)
}
}
cor.4gene<-as.data.frame(cor.4gene)%>%filter(V1 !=0)
colnames(cor.4gene)<-c("gene1","gene2","cor","P")
Can you tell me what mistakes I made?
first, why cor is NA when calculation of correlation for g1 and g1, I though it
should be 1.
cor.4gene$cor[is.na(cor.4gene$cor)]<-1
cor.4gene$cor[is.na(cor.4gene$P)]<-0
cor.4gene.sq <-pivot_wider(cor.4gene, names_from = gene1, values_from = cor)
Then this line of code above did not generate a square matrix as what the HMisc
library did.
How to fix my code?
Thank you,
Ding
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or
entity to which they are addressed. This communication may contain information
that is privileged, confidential, or exempt from disclosure under applicable
law (e.g., personal health information, research data, financial information).
Because this e-mail has been sent without encryption, individuals other than
the intended recipient may be able to view the information, forward it to
others or tamper with the information without the knowledge or consent of the
sender. If you are not the intended recipient, or the employee or person
responsible for delivering the message to the intended recipient, any
dissemination, distribution or copying of the communication is strictly
prohibited. If you received the communication in error, please notify the
sender immediately by replying to this message and deleting the message and any
accompanying files from your system. If, due to the security risks, you do not
wish to rec
eive further communications via e-mail, please reply to this message and
inform the sender that you do not wish to receive further e-mail from the
sender. (LCP301)
------------------------------------------------------------
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
