r - Append to list of lists in for loop -


i have 2 data frames:

data<-structure(list(sample = structure(c(1l, 2l, 2l, 1l, 1l, 1l, 1l,                                               2l, 2l, 2l), .label = c("s1", "s2"), class = "factor"), chrom = structure(c(1l,                                                                                                                           1l, 1l, 2l, 2l, 2l, 1l, 1l, 1l, 2l), .label = c("2l", "2r"), class = "factor"),                          pos = c(318351l, 605574l, 1014043l, 2031592l, 2886957l, 2910379l,                                  2218351l, 105574l, 1344043l, 216957l)), .names = c("sample",                                                                                     "chrom", "pos"), row.names = c(na, 10l), class = "data.frame")  > arrange(data, chrom,sample)     sample chrom     pos 1      s1    2l  318351 2      s1    2l 2218351 3      s2    2l  605574 4      s2    2l 1014043 5      s2    2l  105574 6      s2    2l 1344043 7      s1    2r 2031592 8      s1    2r 2886957 9      s1    2r 2910379 10     s2    2r  216957 
svbreaks<-structure(list(sample = structure(c(1l, 1l, 1l, 2l, 2l, 2l, 1l,                                               1l, 2l, 1l), .label = c("s1", "s2"), class = "factor"), chrom = structure(c(1l,                                                                                                                           1l, 1l, 1l, 1l, 1l, 2l, 2l, 2l, 2l), .label = c("2l", "2r"), class = "factor"),                          bp = c(2425901l, 2426025l, 6694426l, 6694566l, 8387755l,                                 8387927l, 8963713l, 963799l, 980364l, 980521l), gene = structure(c(3l,                                                                                                    3l, 5l, 5l, 4l, 4l, 2l, 2l, 1l, 1l), .label = c("cg8213",                                                                                                                                                    "cg8216", "intergenic", "pdm3", "tsp"), class = "factor"),                          type = structure(c(2l, 1l, 2l, 1l, 3l, 3l, 3l, 4l, 4l, 3l                          ), .label = c("del", "dup", "inv", "tandup"), class = "factor")), row.names = c(na,                                                                                                          10l), .names = c("sample", "chrom", "bp", "gene", "type"), class = "data.frame")  > arrange(svbreaks, chrom, sample)   sample chrom      bp       gene   type 1      s1    2l 2425901 intergenic    dup 2      s1    2l 2426025 intergenic    del 3      s1    2l 6694426        tsp    dup 4      s2    2l 6694566        tsp    del 5      s2    2l 8387755       pdm3    inv 6      s2    2l 8387927       pdm3    inv 7      s1    2r 8963713     cg8216    inv 8      s1    2r  963799     cg8216 tandup 9      s1    2r  980521     cg8213    inv 10     s2    2r  980364     cg8213 tandup

and function calculates distance between pos in data , bp in svbreaks on same chrom each sample:

fun3 <- function(p) {   index<-which.min(abs(sv_df$bp - p))   closestbp<-as.numeric(sv_df$bp[index])   chrom<-as.character(sv_df$chrom[index])   gene<-as.character(sv_df$gene[index])   sample<-as.character(sv_df$sample[index])   type<-as.character(sv_df$type[index])    dist<-(p-closestbp)   list(p, closestbp, dist, chrom, gene, type, sample) }

i want loop through each chrom, , call function each sample , build data frame containing samples , chroms. here's i've got far:

l <- list()  (c in levels(data$chrom)){   (s in levels(data$sample)){     # filter in chromosome , sample     df<-filter(data, chrom == c & sample == s)     sv_df<-filter(svbreaks, chrom == c & sample == s)      # apply funciton     dist2bp<-lapply(df$pos, fun3)      dist2bp<-do.call(rbind, dist2bp)     dist2bp<-as.data.frame(dist2bp)      colnames(dist2bp)=c("snp", "closest_bp", "min_dist", "chrom", "closest_gene", "type", "sample")     l[[s]] <- dist2bp   } }

however, not give me expected output, , saves second level of chrom - here's resulting data frame:

> levels(data$chrom) [1] "2l" "2r" > levels(data$sample) [1] "s1" "s2"           snp closest_bp min_dist chrom closest_gene   type sample s1.1 2031592     980521  1051071    2r       cg8213    inv     s1 s1.2 2886957     980521  1906436    2r       cg8213    inv     s1 s1.3 2910379     980521  1929858    2r       cg8213    inv     s1 s2    216957     980364  -763407    2r       cg8213 tandup     s2

if add list in chrom loop, output not correct: 

for (c in levels(data$chrom)){   (s in levels(data$sample)){     [...]     l[[s]] <- dist2bp   }   l[[c]] <- dist2bp }  snp closest_bp min_dist chrom closest_gene   type sample s1.1 2031592     980521  1051071    2r       cg8213    inv     s1 # chrom level 2, s1 s1.2 2886957     980521  1906436    2r       cg8213    inv     s1 s1.3 2910379     980521  1929858    2r       cg8213    inv     s1 s2    216957     980364  -763407    2r       cg8213 tandup     s2 # chrom level 2, s2 2l.1  605574    6694566 -6088992    2l          tsp    del     s2 # chrom level 1, s2 2l.2 1014043    6694566 -5680523    2l          tsp    del     s2 2l.3  105574    6694566 -6588992    2l          tsp    del     s2 2l.4 1344043    6694566 -5350523    2l          tsp    del     s2 2r    216957     980364  -763407    2r       cg8213 tandup     s2 # not sure why here, # chrom level 1, s1 missing

can point me in right direction?


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