r - For-loop of rownames input to function -
i have function trycatch outputs this:
> s1 <- trycatch(survdiff(surv(as.numeric(as.character(clinicaldatahep$new_death))[ind_clin],clinicaldatahep$death_event[ind_clin])~event_rna[ind_gene,ind_tum]), error = function(e) return(na)) > s1 call: survdiff(formula = surv(as.numeric(as.character(clinicaldatahep$new_death))[ind_clin], clinicaldatahep$death_event[ind_clin]) ~ event_rna[ind_gene, ind_tum]) n observed expected (o-e)^2/e (o-e)^2/v event_rna[ind_gene, ind_tum]=0 72 41 41.1 0.000223 0.00278 event_rna[ind_gene, ind_tum]=1 4 4 3.9 0.002345 0.00278 chisq= 0 on 1 degrees of freedom, p= 0.958 from output possible calculate p-value this:
> p.val <- 1 - pchisq(s1$chisq, length(s1$n) - 1) > p.val [1] 0.9579535 i make for-loop in first function takes possible ind_gene in trycatch defined rownames(matrix_cpm_spike_liver) , get p-values different rownames. examples of ind_gene:
> head(rownames(matrix_cpm_spike_liver)) [1] "hsa-let-7a-2-3p" "hsa-let-7a-3p" "hsa-let-7a-5p" "hsa-let-7b-3p" "hsa-let-7b-5p" [6] "hsa-let-7c-3p" something like:
for (i in rownames(matrix_cpm_spike_liver)) {trycatch... }
one way of doing wrapping function around , use sapply. way not have change code much. make loop successful, must handle cases trycatch catches error. done ifelse on p-value.
mycatch <- function(ind_gene){ s1 <- trycatch(survdiff(surv(as.numeric(as.character( clinicaldatahep$new_death) )[ind_clin], clinicaldatahep$death_event[ind_clin]) ~ event_rna[ind_gene,ind_tum]), error = function(e) return(na)) p.val <- ifelse(is.na(s1), # condition na, # return if s1 = na 1 - pchisq(s1$chisq, length(s1$n) - 1)) p.val } sapply(rownames(matrix_cpm_spike_liver), mycatch) notice how have split lines of code - considered practice not have long lines of code. use max of 65 since paste tex documents can see grey box above, can wider.
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