CODEWITHSUNDEEP
rmatrixrowstrsplitcol
Sajad Shahbazi
Sajad Shahbazi

Reputation: 1

question regarding changing tile of rows and columns of a big matrix

I have a complex names of big matrix. I'm supposed to replace the name by splitting the name of each column which are separated by "_".

sample of name
d__Bacteria.p__Firmicutes.c__Clostridia.o__Lachnospirales.f__Lachnospiraceae.g__Tuzzerella.__

now my target is to extract only family name of each group ending "aceae" (number 6 name) in all columns names and replace instead of such a big complex name.

may I ask you to help me?

I made vectors of columns and rows, and used library(stringr) strsplit(colname_matrix, "_")

I have a list of split names but I do not know how I remove the rest and just keep names ending with "aceae" and apply it for all names in columns and rows. matrix is symmetrical

Upvotes: 0

Views: 50

Answers (1)

chris jude
chris jude

Reputation: 498

x<-"d__Bacteria.p__Firmicutes.c__Clostridia.o__Lachnospirales.f__Lachnospiraceae.g__Tuzzerella.__ "
library(stringr)
str_extract(x, "(?<=f__)[^.g]+")

Base R if u do not want "aceae"

sub(".*.f__","",sub("aceae.*", "", x))

or

y<-as.vector(str_split(x,"__"))
y[[1]][str_detect(y[[1]], "aceae")]

Upvotes: 0

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