#Entered Metadata into a excel file of Ross Conrad virus data and saved as a csv file.
# TITLE: Colony Virus Results for Apiary 125
# DATE: 2016-11-02
# AUTHOR: Samantha Alger
# ------------------------------------------------
# AUTHOR EMAIL: salger@uvm.edu
# AUTHOR ADDRESS: 109 Carrigan Dr., Burlington, VT 05401"
# AUTHOR WEBSITE: NA
# ------------------------------------------------
# OWNERSHIP: Samantha Alger
# COLLABORATORS: Alex Burnham, Ross Conrad"
# FUNDING SOURCES: NA
# REPOSITORY: GitHub, repo: AlgerProjects"
# CITATIONS: NA
# ------------------------------------------------
# SAMPLING LOCATIONS: Apiary '125' (Ross Conrad's apiary)
# SAMPLING TIMES: 2017-08-18
# VARIABLE DESCRIPTION: Sample name is "RC"" for Ross Conrad and unique hive number. Target name is DWV (virus of interest), Ctmean, Ctsd, quantity mean, and quantity sd are from qPCR results. Run is the qPCR run #. dil. factor is the dilution of RNA used in PCR. genome copies is the target copies without reference gene. ACT genome copies is the reference genome copy number, norm genome copy is the normalized copies of DWV in each bee sample. Colony number is the unique ID given to each colony tested.
# MISSING DATA: Hive # 6 was not sampled
#Read in data
RC <- read.table("RossConradDF_Metadata_Exercise.csv", header=TRUE, sep = ",", stringsAsFactors = F)
str(RC)
## 'data.frame': 11 obs. of 12 variables:
## $ sample_name : chr "RC1" "RC2" "RC3" "RC4" ...
## $ target_name : chr "DWV" "DWV" "DWV" "DWV" ...
## $ Ct_mean : num 31.7 17.5 24.5 15.6 14.5 ...
## $ Ct_sd : num 0.328 0.05 0.061 0.001 0.157 0.173 0.103 0.345 0.165 0.186 ...
## $ quantity_mean : num 4.26 9.61e+04 1.05e+03 3.30e+05 6.77e+05 ...
## $ quantity_sd : num 6.02 3134.6 41.49 154.96 68867.83 ...
## $ run : int 68 68 68 68 68 68 68 68 68 68 ...
## $ dil.factor : num 2.5 1.8 1.4 2.8 9.9 1 4.8 1.9 1 5.5 ...
## $ genome_copbee_HB : num 2.66e+03 4.33e+07 3.68e+05 2.31e+08 1.68e+09 ...
## $ ACT_genome_copbee : num 8429514 6273720 3635529 19038870 57602474 ...
## $ norm_genome_copbee: num 5.76e+03 1.26e+08 1.85e+06 2.21e+08 5.31e+08 ...
## $ Colony_Number : int 1 2 3 4 5 7 8 9 10 11 ...
summary(RC)
## sample_name target_name Ct_mean Ct_sd
## Length:11 Length:11 Min. :14.49 Min. :0.0010
## Class :character Class :character 1st Qu.:16.55 1st Qu.:0.0555
## Mode :character Mode :character Median :19.72 Median :0.1570
## Mean :21.93 Mean :0.1445
## 3rd Qu.:27.77 3rd Qu.:0.1795
## Max. :31.68 Max. :0.3450
## quantity_mean quantity_sd run dil.factor
## Min. : 4.3 Min. : 1.59 Min. :68 Min. :1.000
## 1st Qu.: 532.7 1st Qu.: 23.75 1st Qu.:68 1st Qu.:1.600
## Median : 22900.1 Median : 154.96 Median :68 Median :2.400
## Mean :151822.2 Mean :10827.86 Mean :68 Mean :3.182
## 3rd Qu.:212861.3 3rd Qu.: 7574.20 3rd Qu.:68 3rd Qu.:3.800
## Max. :677248.4 Max. :68867.83 Max. :68 Max. :9.900
## genome_copbee_HB ACT_genome_copbee norm_genome_copbee
## Min. :2.661e+03 Min. : 2737731 Min. : 5760
## 1st Qu.:1.938e+05 1st Qu.: 6956158 1st Qu.: 935732
## Median :5.725e+06 Median : 8790390 Median : 12157676
## Mean :2.333e+08 Mean :18244189 Mean :111106474
## 3rd Qu.:1.370e+08 3rd Qu.:26571080 3rd Qu.:173445301
## Max. :1.676e+09 Max. :57602474 Max. :530892519
## Colony_Number
## Min. : 1.000
## 1st Qu.: 3.500
## Median : 7.000
## Mean : 6.545
## 3rd Qu.: 9.500
## Max. :12.000
table(RC$sample_name)
##
## RC1 RC10 RC11 RC12 RC2 RC3 RC4 RC5 RC7 RC8 RC9
## 1 1 1 1 1 1 1 1 1 1 1
head(RC)
## sample_name target_name Ct_mean Ct_sd quantity_mean quantity_sd run
## 1 RC1 DWV 31.682 0.328 4.258 6.022 68
## 2 RC2 DWV 17.500 0.050 96143.540 3134.602 68
## 3 RC3 DWV 24.477 0.061 1050.470 41.487 68
## 4 RC4 DWV 15.597 0.001 329579.060 154.963 68
## 5 RC5 DWV 14.489 0.157 677248.400 68867.830 68
## 6 RC7 DWV 19.721 0.173 22900.129 2552.953 68
## dil.factor genome_copbee_HB ACT_genome_copbee norm_genome_copbee
## 1 2.5 2.661250e+03 8429514 5.759804e+03
## 2 1.8 4.326459e+07 6273720 1.258149e+08
## 3 1.4 3.676645e+05 3635529 1.845052e+06
## 4 2.8 2.307053e+08 19038870 2.210757e+08
## 5 9.9 1.676190e+09 57602474 5.308925e+08
## 6 1.0 5.725032e+06 7638596 1.367379e+07
## Colony_Number
## 1 1
## 2 2
## 3 3
## 4 4
## 5 5
## 6 7
tail(RC)
## sample_name target_name Ct_mean Ct_sd quantity_mean quantity_sd run
## 6 RC7 DWV 19.721 0.173 22900.129 2552.953 68
## 7 RC8 DWV 15.005 0.103 484192.700 32266.447 68
## 8 RC9 DWV 18.404 0.345 54221.227 12013.800 68
## 9 RC10 DWV 31.057 0.165 14.872 1.588 68
## 10 RC11 DWV 31.096 0.186 14.516 1.742 68
## 11 RC12 DWV 22.171 0.021 4674.575 65.029 68
## dil.factor genome_copbee_HB ACT_genome_copbee norm_genome_copbee
## 6 1.0 5725032.2 7638596 13673790.94
## 7 4.8 581031240.0 34103290 310833461.00
## 8 1.9 25755082.8 38648883 12157675.71
## 9 1.0 3718.0 2737731 24776.69
## 10 5.5 19959.5 13787077 26412.04
## 11 2.4 2804745.0 8790390 5821163.43
## Colony_Number
## 6 7
## 7 8
## 8 9
## 9 10
## 10 11
## 11 12