You can use
## S3 method for class 'data.frame'
aggregate(x, by, FUN, ..., simplify = TRUE)
With your data assuming your data is in dataframe DF
DF <- read.table(text = txt, header = FALSE, stringsAsFactors = FALSE)
result <- aggregate(DF[, 9:118], by = list(DF[, 4]), FUN = mean)
# Using pander to print result table nicely. It's not needed for aggregation :)
require(pander)
pandoc.table(result)
##
## ----------------------------------------------------
## Group.1 V9 V10 V11 V12 V13 V14
## ---------------- ----- ----- ----- ----- ----- -----
## 5'to3'ExonIntron 161.9 148 131 122.7 109.7 98.1
##
## 5'to3'IntronExon 0.0 0 0 0.0 0.0 0.0
## ----------------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V15 V16 V17 V18 V19 V20 V21 V22
## ----- ----- ----- ----- ----- ----- ----- -----
## 81.5 66.6 52.3 39.5 26.1 18.7 12.4 9.3
##
## 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V23 V24 V25 V26 V27 V28 V29 V30
## ----- ----- ----- ----- ----- ----- ----- -----
## 7.2 4.6 1.8 0.4 0 0 0 0.5
##
## 0.0 0.0 0.0 0.0 0 0 0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V31 V32 V33 V34 V35 V36 V37 V38
## ----- ----- ----- ----- ----- ----- ----- -----
## 0.9 1.5 1.8 2.4 2.7 5 6.4 9.1
##
## 0.0 0.0 0.0 0.0 0.0 0 0.0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V39 V40 V41 V42 V43 V44 V45 V46
## ----- ----- ----- ----- ----- ----- ----- -----
## 13 16.2 19.2 21.5 23 24.7 28 29.7
##
## 0 0.0 0.0 0.0 0 0.0 0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V47 V48 V49 V50 V51 V52 V53 V54
## ----- ----- ----- ----- ----- ----- ----- -----
## 36.9 45.7 59.5 73.3 89.2 101.3 106.2 114
##
## 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V55 V56 V57 V58 V59 V60 V61 V62
## ----- ----- ----- ----- ----- ----- ----- -----
## 127.3 134 140.7 148.1 156.2 160.4 167.4 175.7
##
## 0.0 0 0.0 0.0 0.0 0.0 0.0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V63 V64 V65 V66 V67 V68 V69 V70
## ----- ----- ----- ----- ----- ----- ----- -----
## 183.9 183.1 183.7 182.3 178.1 169 163.8 156.7
##
## 0.0 0.0 0.0 0.0 0.0 0 0.0 0.0
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V71 V72 V73 V74 V75 V76 V77 V78
## ----- ----- ----- ----- ----- ----- ----- -----
## 149.8 126.6 86.3 74.0 64.0 59.8 56.0 50.6
##
## 0.7 0.9 0.9 1.5 1.8 1.8 1.8 1.8
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V79 V80 V81 V82 V83 V84 V85 V86
## ----- ----- ----- ----- ----- ----- ----- -----
## 45.6 42.2 38.7 31.9 24.9 18.6 14.1 9.4
##
## 1.8 1.8 1.8 1.8 1.8 1.8 2.2 2.7
## -----------------------------------------------
##
## Table: Table continues below
##
##
## -----------------------------------------------
## V87 V88 V89 V90 V91 V92 V93 V94
## ----- ----- ----- ----- ----- ----- ----- -----
## 7.6 6.2 5.1 3.7 2.9 2.5 2.7 2.7
##
## 2.7 2.7 2.7 2.7 2.7 2.7 2.2 0.9
## -----------------------------------------------
##
## Table: Table continues below
##
##
## --------------------------------------------------
## V95 V96 V97 V98 V99 V100 V101 V102
## ----- ----- ----- ----- ----- ------ ------ ------
## 4.2 4.5 4.5 4.5 4.5 4.5 4.3 2.5
##
## 0.9 0.9 0.9 1.4 4.1 5.4 6.9 10.6
## --------------------------------------------------
##
## Table: Table continues below
##
##
## -------------------------------------------------------
## V103 V104 V105 V106 V107 V108 V109 V110
## ------ ------ ------ ------ ------ ------ ------ ------
## 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.8
##
## 13.7 18.4 30.2 40.4 53.3 63.0 77.3 90.3
## -------------------------------------------------------
##
## Table: Table continues below
##
##
## -------------------------------------------------------
## V111 V112 V113 V114 V115 V116 V117 V118
## ------ ------ ------ ------ ------ ------ ------ ------
## 1.8 1.8 1.8 1.8 1.4 0.5 0.0 0.0
##
## 104.5 117.3 134.3 147.8 164.8 181.0 189.4 199.2
## -------------------------------------------------------
##