Replace values in column using logical vector
I have a dataframe in long form. The OTU column has ~428 unique ids with repeated measures resulting in 26,536 rows.
'data.frame': 26536 obs. of 18 variables:
$ OTU : chr "109431" "109431" "109431" "109431" ...
$ Sample : chr "m.ch.45" "m.ch.59" "m.ch.85" "m.ch.51" ...
$ Abundance : num 0.994 0.983 0.981 0.975 0.975 ...
$ X.SampleID : Factor w/ 62 levels "m.ch.1","m.ch.101",..: 28 37 52 33
8 15 13 7 58 14 ...
$ Family : Factor w/ 89 levels
"f__","f__[Acidaminobacteraceae]",..: 26 26 26 26 26 26 26 26 26 26
...
Of the unique ids in column OTU, I want to focus on 9 of them (top9names).
I made a logical vector with all OTUs in the top 9 as TRUE and all those that are not as FALSE
matches <- qd_melted$OTU %in% top9names
For these 9 OTU names I want to preserve the corresponding Family name (column5). For the other OTU names (~419), I want to replace the value in the Family column with "Other taxa".
Any tips on how to code this?
r dataframe replace
edited Nov 13 '18 at 4:36
Shree
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
add a comment |
I have a dataframe in long form. The OTU column has ~428 unique ids with repeated measures resulting in 26,536 rows.
'data.frame': 26536 obs. of 18 variables:
$ OTU : chr "109431" "109431" "109431" "109431" ...
$ Sample : chr "m.ch.45" "m.ch.59" "m.ch.85" "m.ch.51" ...
$ Abundance : num 0.994 0.983 0.981 0.975 0.975 ...
$ X.SampleID : Factor w/ 62 levels "m.ch.1","m.ch.101",..: 28 37 52 33
8 15 13 7 58 14 ...
$ Family : Factor w/ 89 levels
"f__","f__[Acidaminobacteraceae]",..: 26 26 26 26 26 26 26 26 26 26
...
Of the unique ids in column OTU, I want to focus on 9 of them (top9names).
I made a logical vector with all OTUs in the top 9 as TRUE and all those that are not as FALSE
matches <- qd_melted$OTU %in% top9names
For these 9 OTU names I want to preserve the corresponding Family name (column5). For the other OTU names (~419), I want to replace the value in the Family column with "Other taxa".
Any tips on how to code this?
r dataframe replace
edited Nov 13 '18 at 4:36
Shree
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
add a comment |
I have a dataframe in long form. The OTU column has ~428 unique ids with repeated measures resulting in 26,536 rows.
'data.frame': 26536 obs. of 18 variables:
$ OTU : chr "109431" "109431" "109431" "109431" ...
$ Sample : chr "m.ch.45" "m.ch.59" "m.ch.85" "m.ch.51" ...
$ Abundance : num 0.994 0.983 0.981 0.975 0.975 ...
$ X.SampleID : Factor w/ 62 levels "m.ch.1","m.ch.101",..: 28 37 52 33
8 15 13 7 58 14 ...
$ Family : Factor w/ 89 levels
"f__","f__[Acidaminobacteraceae]",..: 26 26 26 26 26 26 26 26 26 26
...
Of the unique ids in column OTU, I want to focus on 9 of them (top9names).
I made a logical vector with all OTUs in the top 9 as TRUE and all those that are not as FALSE
matches <- qd_melted$OTU %in% top9names
For these 9 OTU names I want to preserve the corresponding Family name (column5). For the other OTU names (~419), I want to replace the value in the Family column with "Other taxa".
Any tips on how to code this?
r dataframe replace
edited Nov 13 '18 at 4:36
Shree
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
I have a dataframe in long form. The OTU column has ~428 unique ids with repeated measures resulting in 26,536 rows.
'data.frame': 26536 obs. of 18 variables:
$ OTU : chr "109431" "109431" "109431" "109431" ...
$ Sample : chr "m.ch.45" "m.ch.59" "m.ch.85" "m.ch.51" ...
$ Abundance : num 0.994 0.983 0.981 0.975 0.975 ...
$ X.SampleID : Factor w/ 62 levels "m.ch.1","m.ch.101",..: 28 37 52 33
8 15 13 7 58 14 ...
$ Family : Factor w/ 89 levels
"f__","f__[Acidaminobacteraceae]",..: 26 26 26 26 26 26 26 26 26 26
...
Of the unique ids in column OTU, I want to focus on 9 of them (top9names).
I made a logical vector with all OTUs in the top 9 as TRUE and all those that are not as FALSE
matches <- qd_melted$OTU %in% top9names
For these 9 OTU names I want to preserve the corresponding Family name (column5). For the other OTU names (~419), I want to replace the value in the Family column with "Other taxa".
Any tips on how to code this?
r dataframe replace
r dataframe replace
edited Nov 13 '18 at 4:36
Shree
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
edited Nov 13 '18 at 4:36
Shree
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
edited Nov 13 '18 at 4:36
Shree
3,3111323
edited Nov 13 '18 at 4:36
Shree
3,3111323
edited Nov 13 '18 at 4:36
Shree
3,3111323
3,3111323
asked Nov 13 '18 at 2:11
BeccaBecca
244
asked Nov 13 '18 at 2:11
BeccaBecca
244
asked Nov 13 '18 at 2:11
BeccaBecca
244
244
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
When adding a new value to factors you need to update the levels first. Here's one way -
levels(qd_melted$Family) <- c(levels(qd_melted$Family), "Other taxa")
qd_melted$Family[!matches] <- "Other taxa"
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
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
When adding a new value to factors you need to update the levels first. Here's one way -
levels(qd_melted$Family) <- c(levels(qd_melted$Family), "Other taxa")
qd_melted$Family[!matches] <- "Other taxa"
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
add a comment |
When adding a new value to factors you need to update the levels first. Here's one way -
levels(qd_melted$Family) <- c(levels(qd_melted$Family), "Other taxa")
qd_melted$Family[!matches] <- "Other taxa"
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
add a comment |
When adding a new value to factors you need to update the levels first. Here's one way -
levels(qd_melted$Family) <- c(levels(qd_melted$Family), "Other taxa")
qd_melted$Family[!matches] <- "Other taxa"
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
When adding a new value to factors you need to update the levels first. Here's one way -
levels(qd_melted$Family) <- c(levels(qd_melted$Family), "Other taxa")
qd_melted$Family[!matches] <- "Other taxa"
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
answered Nov 13 '18 at 2:26
ShreeShree
3,3111323
3,3111323
add a comment |
add a comment |
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