filtering dataframe using multiple columns in R
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Entering edit mode
3.5 years ago

Hi guys,

So, i have this dataframe (for e.g.):

   CGDid           Mass      Source.File        pepSeq
 C1_00060W_A    5117.5552   T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00060W_A    5117.5552   T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00060W_A    5117.5552   T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00061W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00063W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00062W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A

And the thing is i want to filter when the columns CGDid, Mass, pepSeq are equal and the Source.File is different. I am trying to figure out the best way to this but i am blocked. I will be very appreciate if someone could help me!

All the best, Andreia
filter R dataframe • 1.3k views
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Thank you all :)

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3.5 years ago
Zhilong Jia ★ 2.2k 
t1 <- readr::read_tsv("./1.t")
dplyr::group_by(t1, CGDid, Mass, pepSeq)  %>% dplyr::distinct(Source.File)

output:

# A tibble: 9 x 4
# Groups:   CGDid, Mass, pepSeq [6]
  CGDid       Mass Source.File   pepSeq                                         
  <chr>      <dbl> <chr>         <chr>                                          
1 C1_00060W… 5118. T0_4_excl.raw NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK 
2 C1_00060W… 5118. T0_4.raw      NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK 
3 C1_00061W… 6304. T0_4.raw      NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK…
4 C1_00060W… 6304. T0_4.raw      NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK…
5 C1_00060W… 6304. T0_4_excl.raw NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK…
6 C1_00063W… 6304. T0_4.raw      NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK…
7 C1_00060W… 6305. T0_4_excl.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVI…
8 C1_00060W… 6305. T0_4.raw      K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVI…
9 C1_00062W… 6305. T0_4.raw      K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVI…
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3.5 years ago
zx8754 12k

Using aggregate:

aggregate(Source.File ~ CGDid + Mass + pepSeq, data = d,
          FUN = function(x) { c(names = toString(unique(x)),
                                count = length(unique(x))) })
#         CGDid     Mass                                                       pepSeq       Source.File.names Source.File.count
# 1 C1_00060W_A 6305.149 K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A T0_4_excl.raw, T0_4.raw                 2
# 2 C1_00062W_A 6305.149 K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A                T0_4.raw                 1
# 3 C1_00060W_A 5117.555               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK T0_4_excl.raw, T0_4.raw                 2
# 4 C1_00060W_A 6304.165     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR T0_4.raw, T0_4_excl.raw                 2
# 5 C1_00061W_A 6304.165     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR                T0_4.raw                 1
# 6 C1_00063W_A 6304.165     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR                T0_4.raw                 1


# example data
d <- read.table(text = "   CGDid           Mass      Source.File        pepSeq
 C1_00060W_A    5117.5552   T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00060W_A    5117.5552   T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00060W_A    5117.5552   T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 C1_00061W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00063W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4.raw        NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6304.165    T0_4_excl.raw   NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00062W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4.raw        K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
 C1_00060W_A    6305.1489   T0_4_excl.raw   K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A",
 header = TRUE)
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Entering edit mode
3.5 years ago
PKW ▴ 110 
library(data.table)
df= fread("data.txt", sep = " ", header = T)` 


            CGDid     Mass   Source.File                                                       pepSeq
 1: C1_00060W_A 5117.555 T0_4_excl.raw               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 2: C1_00060W_A 5117.555      T0_4.raw               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 3: C1_00060W_A 5117.555      T0_4.raw               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
 4: C1_00061W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 5: C1_00060W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 6: C1_00060W_A 6304.165 T0_4_excl.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 7: C1_00063W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 8: C1_00060W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
 9: C1_00060W_A 6304.165 T0_4_excl.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
10: C1_00060W_A 6305.149 T0_4_excl.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
11: C1_00060W_A 6305.149 T0_4_excl.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
12: C1_00060W_A 6305.149      T0_4.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
13: C1_00062W_A 6305.149      T0_4.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
14: C1_00060W_A 6305.149      T0_4.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
15: C1_00060W_A 6305.149 T0_4_excl.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A


df= unique(df)

         CGDid     Mass   Source.File                                                       pepSeq
1: C1_00060W_A 5117.555 T0_4_excl.raw               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
2: C1_00060W_A 5117.555      T0_4.raw               NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDK
3: C1_00061W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
4: C1_00060W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
5: C1_00060W_A 6304.165 T0_4_excl.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
6: C1_00063W_A 6304.165      T0_4.raw     NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR
7: C1_00060W_A 6305.149 T0_4_excl.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
8: C1_00060W_A 6305.149      T0_4.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
9: C1_00062W_A 6305.149      T0_4.raw K.NGFQQQQQQQQQQQQQQQQQQQQIVAPPAAPPAPPTPVTSLSVIDKSQYIVNPTQR.A
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