GCalignR 的 R 预处理数据中的字符串拆分问题
[英]String split issue in R preprocessing data for GCalignR
问题描述
Trying to take multiple .txt (GC-FID) files, pull out two columns of data and assign them to an object I can eventually pass to GCalignR.
尝试获取多个 .txt (GC-FID) 文件，提取两列数据并将它们分配给我最终可以传递给 GCalignR 的对象。 Is there a better way to process this data for GCalignR?有没有更好的方法来处理 GCalignR 的这些数据？
Auxiliary functions causing issue:导致问题的辅助功能：
''' '''
# nonempty strings after splitting a row by one space
get_nonempty_splits = function(row) {
s = strsplit(row, "[[:space:]]")
s = s[[1]]
l = c()
for (i in 1:length(s)) {
if (s[i] != "") {
l = c(l, s[i])
}
}
return(l)
}
# filenames have .txt, names do not
filenames_to_names = function(x) {
l = c()
for (i in 1:length(x)) {
x1 = strsplit(x, "[.]")[[i]][1]
l = c(l, x1)
}
return(l)
}
# get data row indices
get_data_row_inds = function(df) {
ind_start = 0
ind_end = 0
for (i in 1:length(df)) {
row = df[i]
# find start
if (grepl("----", row)) {
stopifnot(ind_start == 0) # assert ind_start not set
ind_start = i+1
}
# find end
if (i == length(df) && ind_end == 0) {
ind_end = length(df)
} else if (grepl("Totals", row) && grepl(":", row)) {
stopifnot(ind_end == 0) # assert ind_end not set
ind_end = i-1
}
}
stopifnot(ind_start != 0)
stopifnot(ind_end != 0)
return(ind_start:ind_end)
}
''' '''
''' '''
path_to_raw_data = "/Users/input"
path_to_processed_data = "."
# get paths for all .txt files in pathToRawData directory
paths = list.files(path_to_raw_data, full.name=TRUE, pattern = ".txt")
filenames = list.files(path_to_raw_data, full.name=FALSE, pattern = ".txt")
names = filenames_to_names(filenames) # without .txt extension
# get data from text file
processed_data = list()
df_lengths = c()
for (i in 1:length(paths)) { # i indexes the raw files
path = paths[i]
df = read.delim(path, fileEncoding= 'UTF-16LE', header=TRUE)
df = df[[1]]
inds = get_data_row_inds(df)
df_lengths = c(df_lengths, length(inds))
times = c()
areas = c()
for (j in inds) { # j indexes the data rows of a raw file
row = df[j]
row = get_nonempty_splits(row)
time = row_to_time(row)
area = row_to_area(row)
times = c(times, time)
areas = c(areas, area)
}
pairs = data.frame(time = times, area = areas)
processed_data[[i]] = pairs
}
''' '''
Getting this error: Error in strsplit(row, "[[:space:]]") : non-character argument收到此错误： strsplit(row, "[[:space:]]") 中的错误：非字符参数
Any advice how to solve this?任何建议如何解决这个问题？ Is it the file encoding?是文件编码吗？ Processed-data =list() returns nothing...? Processed-data =list() 什么都不返回...？
header of input: '''输入标题：'''
dput(head(df)) structure(c(59L, 53L, 45L, 48L, 47L, 52L), .Label = c(" Inj Volume : 1 µl", " *** End of Report ***", " Area Percent Report ", " 1 1.353 1 BB 2.85703 2.453e-5 ? ", " 2 1.952 1 BV 4411.39551 0.03787 ? ", " 3 2.058 1 VV 4693.20215 0.04029 ? ", " 4 2.089 1 VV 6614.89502 0.05679 ? ", " 5 2.139 2 0.00000 0.00000 NG ", " 6 2.452 2 0.00000 0.00000 1, 3-DNB ", " 7 3.149 2 0.00000 0.00000 2, 4-DNT ", " 8 3.315 1 VV S 1.15784e7 99.39858 ? ", " 9 3.347 1 VV S 5169.44629 0.04438 ? ", " # [min] %", " 10 3.372 1 VV S 2.09449e4 0.17981 ? ", " 11 3.466 1 VV S 2535.17432 0.02176 ? ", " 12 3.547 1 VB S 2.45685e4 0.21092 ? ", " 13 3.602 1 BV T 451.00174 0.00387 ? ", " 14 3.686 1 VV T 40.45324 0.00035 ? ", " 15 3.734 1 VV T 13.40936 0.00012 ? ", " 16 3.819 1 VB T 508.57788 0.00437 ? ", " 17 4.119 1 BB 13.01144 0.00011 ? ", " 18 4.856 2 0.00000 0.00000 TNT ", " 19 4.975 2 0.00000 0.00000 TNB ", " 20 5.549 2 0.00000 0.00000 4-Am-DNT ", " 21 5.869 2 0.00000 0.00000 RDX ", " 22 5.943 2 0.00000
1 个解决方案
解决方案1
0 2020-10-12 18:10:30
Solved with adding: df = read.delim(path, fileEncoding= 'UTF-16LE', header=TRUE, stringsAsFactors = FALSE).通过添加解决：df = read.delim(path, fileEncoding='UTF-16LE', header=TRUE, stringsAsFactors = FALSE)。 The "stringsAsFactors = FALSE" being the solution. “stringsAsFactors = FALSE”是解决方案。 Thank you.谢谢你。
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